Starting phenix.real_space_refine on Tue Feb 13 11:45:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wks_32568/02_2024/7wks_32568.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wks_32568/02_2024/7wks_32568.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wks_32568/02_2024/7wks_32568.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wks_32568/02_2024/7wks_32568.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wks_32568/02_2024/7wks_32568.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wks_32568/02_2024/7wks_32568.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 3902 2.51 5 N 938 2.21 5 O 992 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 5874 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 2937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 2937 Classifications: {'peptide': 377} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 359} Chain breaks: 1 Chain: "A" Number of atoms: 2937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 2937 Classifications: {'peptide': 377} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 359} Chain breaks: 1 Time building chain proxies: 3.71, per 1000 atoms: 0.63 Number of scatterers: 5874 At special positions: 0 Unit cell: (79.143, 125.097, 69.782, 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 42 16.00 O 992 8.00 N 938 7.00 C 3902 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 2.22 Conformation dependent library (CDL) restraints added in 1.2 seconds 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1420 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 2 sheets defined 79.0% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'B' and resid 4 through 30 Proline residue: B 16 - end of helix Processing helix chain 'B' and resid 35 through 62 removed outlier: 4.757A pdb=" N VAL B 51 " --> pdb=" O ALA B 47 " (cutoff:3.500A) Proline residue: B 52 - end of helix removed outlier: 3.580A pdb=" N THR B 61 " --> pdb=" O HIS B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 92 removed outlier: 3.611A pdb=" N LYS B 79 " --> pdb=" O ASP B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 110 Processing helix chain 'B' and resid 116 through 125 Processing helix chain 'B' and resid 126 through 143 removed outlier: 3.533A pdb=" N GLY B 130 " --> pdb=" O GLY B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 165 Processing helix chain 'B' and resid 167 through 170 removed outlier: 3.787A pdb=" N ALA B 170 " --> pdb=" O GLU B 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 167 through 170' Processing helix chain 'B' and resid 475 through 492 removed outlier: 4.003A pdb=" N MET B 479 " --> pdb=" O PRO B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 514 removed outlier: 3.561A pdb=" N TYR B 498 " --> pdb=" O ASN B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 530 removed outlier: 4.177A pdb=" N LEU B 528 " --> pdb=" O SER B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 547 Processing helix chain 'B' and resid 554 through 581 removed outlier: 4.278A pdb=" N GLY B 569 " --> pdb=" O ARG B 565 " (cutoff:3.500A) Proline residue: B 570 - end of helix Processing helix chain 'B' and resid 584 through 595 Processing helix chain 'B' and resid 599 through 610 removed outlier: 3.945A pdb=" N PHE B 603 " --> pdb=" O GLY B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 639 removed outlier: 3.577A pdb=" N LEU B 616 " --> pdb=" O HIS B 612 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N LEU B 628 " --> pdb=" O MET B 624 " (cutoff:3.500A) Proline residue: B 629 - end of helix Processing helix chain 'A' and resid 4 through 30 Proline residue: A 16 - end of helix Processing helix chain 'A' and resid 35 through 62 removed outlier: 4.760A pdb=" N VAL A 51 " --> pdb=" O ALA A 47 " (cutoff:3.500A) Proline residue: A 52 - end of helix removed outlier: 3.581A pdb=" N THR A 61 " --> pdb=" O HIS A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 92 removed outlier: 3.612A pdb=" N LYS A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 110 Processing helix chain 'A' and resid 116 through 125 Processing helix chain 'A' and resid 126 through 143 removed outlier: 3.535A pdb=" N GLY A 130 " --> pdb=" O GLY A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 165 Processing helix chain 'A' and resid 167 through 170 removed outlier: 3.767A pdb=" N ALA A 170 " --> pdb=" O GLU A 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 167 through 170' Processing helix chain 'A' and resid 475 through 492 removed outlier: 4.005A pdb=" N MET A 479 " --> pdb=" O PRO A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 514 removed outlier: 3.560A pdb=" N TYR A 498 " --> pdb=" O ASN A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 530 removed outlier: 4.179A pdb=" N LEU A 528 " --> pdb=" O SER A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 547 Processing helix chain 'A' and resid 554 through 581 removed outlier: 4.253A pdb=" N GLY A 569 " --> pdb=" O ARG A 565 " (cutoff:3.500A) Proline residue: A 570 - end of helix Processing helix chain 'A' and resid 584 through 595 Processing helix chain 'A' and resid 599 through 610 removed outlier: 3.950A pdb=" N PHE A 603 " --> pdb=" O GLY A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 639 removed outlier: 3.585A pdb=" N LEU A 616 " --> pdb=" O HIS A 612 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N LEU A 628 " --> pdb=" O MET A 624 " (cutoff:3.500A) Proline residue: A 629 - end of helix Processing sheet with id=AA1, first strand: chain 'B' and resid 172 through 177 removed outlier: 4.581A pdb=" N ILE B 172 " --> pdb=" O LEU B 202 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N VAL B 204 " --> pdb=" O ILE B 172 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N SER B 174 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N VAL B 206 " --> pdb=" O SER B 174 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LYS B 176 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N LYS B 208 " --> pdb=" O LYS B 176 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 172 through 177 removed outlier: 4.596A pdb=" N ILE A 172 " --> pdb=" O LEU A 202 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N VAL A 204 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N SER A 174 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N VAL A 206 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LYS A 176 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N LYS A 208 " --> pdb=" O LYS A 176 " (cutoff:3.500A) 434 hydrogen bonds defined for protein. 1302 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: 1.63 Time building geometry restraints manager: 2.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1770 1.34 - 1.46: 1148 1.46 - 1.58: 3022 1.58 - 1.69: 0 1.69 - 1.81: 78 Bond restraints: 6018 Sorted by residual: bond pdb=" C ASN A 494 " pdb=" O ASN A 494 " ideal model delta sigma weight residual 1.238 1.249 -0.011 1.28e-02 6.10e+03 7.40e-01 bond pdb=" C GLN A 140 " pdb=" O GLN A 140 " ideal model delta sigma weight residual 1.237 1.227 0.010 1.17e-02 7.31e+03 6.72e-01 bond pdb=" C GLN B 140 " pdb=" O GLN B 140 " ideal model delta sigma weight residual 1.237 1.228 0.009 1.17e-02 7.31e+03 5.98e-01 bond pdb=" CA ASN B 112 " pdb=" C ASN B 112 " ideal model delta sigma weight residual 1.525 1.515 0.010 1.25e-02 6.40e+03 5.97e-01 bond pdb=" C ASN B 494 " pdb=" O ASN B 494 " ideal model delta sigma weight residual 1.238 1.248 -0.010 1.28e-02 6.10e+03 5.77e-01 ... (remaining 6013 not shown) Histogram of bond angle deviations from ideal: 99.03 - 106.03: 152 106.03 - 113.02: 3365 113.02 - 120.02: 2037 120.02 - 127.01: 2567 127.01 - 134.01: 79 Bond angle restraints: 8200 Sorted by residual: angle pdb=" N VAL A 14 " pdb=" CA VAL A 14 " pdb=" C VAL A 14 " ideal model delta sigma weight residual 109.34 115.09 -5.75 2.08e+00 2.31e-01 7.65e+00 angle pdb=" N VAL B 14 " pdb=" CA VAL B 14 " pdb=" C VAL B 14 " ideal model delta sigma weight residual 109.34 115.05 -5.71 2.08e+00 2.31e-01 7.55e+00 angle pdb=" N TYR B 125 " pdb=" CA TYR B 125 " pdb=" C TYR B 125 " ideal model delta sigma weight residual 110.80 115.30 -4.50 2.13e+00 2.20e-01 4.46e+00 angle pdb=" N TYR A 125 " pdb=" CA TYR A 125 " pdb=" C TYR A 125 " ideal model delta sigma weight residual 110.80 115.27 -4.47 2.13e+00 2.20e-01 4.41e+00 angle pdb=" CB ARG A 565 " pdb=" CG ARG A 565 " pdb=" CD ARG A 565 " ideal model delta sigma weight residual 111.30 115.38 -4.08 2.30e+00 1.89e-01 3.15e+00 ... (remaining 8195 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 3240 17.96 - 35.92: 251 35.92 - 53.88: 35 53.88 - 71.84: 8 71.84 - 89.80: 4 Dihedral angle restraints: 3538 sinusoidal: 1346 harmonic: 2192 Sorted by residual: dihedral pdb=" CA ASP B 199 " pdb=" CB ASP B 199 " pdb=" CG ASP B 199 " pdb=" OD1 ASP B 199 " ideal model delta sinusoidal sigma weight residual -30.00 -84.89 54.89 1 2.00e+01 2.50e-03 1.02e+01 dihedral pdb=" CA ASP A 199 " pdb=" CB ASP A 199 " pdb=" CG ASP A 199 " pdb=" OD1 ASP A 199 " ideal model delta sinusoidal sigma weight residual -30.00 -84.79 54.79 1 2.00e+01 2.50e-03 1.02e+01 dihedral pdb=" CA ASN B 112 " pdb=" CB ASN B 112 " pdb=" CG ASN B 112 " pdb=" OD1 ASN B 112 " ideal model delta sinusoidal sigma weight residual -90.00 -154.50 64.50 2 2.00e+01 2.50e-03 9.78e+00 ... (remaining 3535 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 635 0.030 - 0.061: 236 0.061 - 0.091: 83 0.091 - 0.121: 28 0.121 - 0.152: 8 Chirality restraints: 990 Sorted by residual: chirality pdb=" CA VAL B 206 " pdb=" N VAL B 206 " pdb=" C VAL B 206 " pdb=" CB VAL B 206 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.75e-01 chirality pdb=" CA VAL A 206 " pdb=" N VAL A 206 " pdb=" C VAL A 206 " pdb=" CB VAL A 206 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.70e-01 chirality pdb=" CA ASN B 112 " pdb=" N ASN B 112 " pdb=" C ASN B 112 " pdb=" CB ASN B 112 " both_signs ideal model delta sigma weight residual False 2.51 2.64 -0.13 2.00e-01 2.50e+01 4.52e-01 ... (remaining 987 not shown) Planarity restraints: 990 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 474 " -0.029 5.00e-02 4.00e+02 4.45e-02 3.17e+00 pdb=" N PRO A 475 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 475 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 475 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 474 " 0.029 5.00e-02 4.00e+02 4.44e-02 3.15e+00 pdb=" N PRO B 475 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 475 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 475 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 564 " 0.009 2.00e-02 2.50e+03 1.73e-02 2.99e+00 pdb=" C VAL B 564 " -0.030 2.00e-02 2.50e+03 pdb=" O VAL B 564 " 0.011 2.00e-02 2.50e+03 pdb=" N ARG B 565 " 0.010 2.00e-02 2.50e+03 ... (remaining 987 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 95 2.71 - 3.26: 5969 3.26 - 3.80: 9380 3.80 - 4.35: 11271 4.35 - 4.90: 19488 Nonbonded interactions: 46203 Sorted by model distance: nonbonded pdb=" O PHE B 105 " pdb=" OG1 THR B 109 " model vdw 2.162 2.440 nonbonded pdb=" O PHE A 105 " pdb=" OG1 THR A 109 " model vdw 2.163 2.440 nonbonded pdb=" O ILE A 492 " pdb=" OH TYR A 498 " model vdw 2.193 2.440 nonbonded pdb=" O ILE B 492 " pdb=" OH TYR B 498 " model vdw 2.193 2.440 nonbonded pdb=" OE1 GLN B 547 " pdb=" OG SER B 617 " model vdw 2.234 2.440 ... (remaining 46198 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.300 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 19.950 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 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:13.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 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 : 0.002 0.023 6018 Z= 0.155 Angle : 0.543 5.752 8200 Z= 0.290 Chirality : 0.038 0.152 990 Planarity : 0.005 0.044 990 Dihedral : 13.066 89.799 2118 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.31), residues: 746 helix: 1.67 (0.22), residues: 558 sheet: 2.09 (0.86), residues: 42 loop : -0.97 (0.53), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 506 HIS 0.001 0.000 HIS B 514 PHE 0.010 0.001 PHE A 566 TYR 0.006 0.001 TYR A 635 ARG 0.008 0.000 ARG B 207 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 0.641 Fit side-chains REVERT: B 610 ASN cc_start: 0.8317 (t0) cc_final: 0.7890 (t0) REVERT: A 160 LEU cc_start: 0.6733 (tt) cc_final: 0.6162 (mt) REVERT: A 610 ASN cc_start: 0.8314 (t0) cc_final: 0.7890 (t0) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 1.1653 time to fit residues: 137.7921 Evaluate side-chains 97 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 0.4980 chunk 56 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.0908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6018 Z= 0.190 Angle : 0.534 6.460 8200 Z= 0.275 Chirality : 0.038 0.141 990 Planarity : 0.004 0.039 990 Dihedral : 4.139 15.223 800 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 1.41 % Allowed : 10.66 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.31), residues: 746 helix: 1.74 (0.22), residues: 564 sheet: 2.02 (0.84), residues: 42 loop : -1.01 (0.54), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 506 HIS 0.001 0.000 HIS A 187 PHE 0.011 0.001 PHE A 92 TYR 0.006 0.001 TYR A 635 ARG 0.001 0.000 ARG A 588 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 107 time to evaluate : 0.717 Fit side-chains REVERT: B 160 LEU cc_start: 0.7058 (tm) cc_final: 0.6043 (mt) REVERT: B 610 ASN cc_start: 0.8302 (t0) cc_final: 0.7926 (t0) REVERT: A 610 ASN cc_start: 0.8296 (t0) cc_final: 0.7924 (t0) outliers start: 9 outliers final: 4 residues processed: 112 average time/residue: 1.1083 time to fit residues: 130.6358 Evaluate side-chains 96 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 92 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 568 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 37 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 55 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 chunk 18 optimal weight: 0.0970 chunk 67 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 54 optimal weight: 8.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 ASN B 472 ASN A 68 ASN A 472 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6018 Z= 0.149 Angle : 0.501 7.254 8200 Z= 0.256 Chirality : 0.036 0.125 990 Planarity : 0.004 0.037 990 Dihedral : 4.013 15.163 800 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 1.25 % Allowed : 14.58 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.31), residues: 746 helix: 1.87 (0.22), residues: 564 sheet: 2.05 (0.84), residues: 42 loop : -0.94 (0.54), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 506 HIS 0.001 0.000 HIS A 5 PHE 0.009 0.001 PHE B 92 TYR 0.005 0.001 TYR A 635 ARG 0.001 0.000 ARG B 512 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 98 time to evaluate : 0.638 Fit side-chains REVERT: B 160 LEU cc_start: 0.7131 (tm) cc_final: 0.6031 (mt) REVERT: B 610 ASN cc_start: 0.8218 (t0) cc_final: 0.7868 (t0) REVERT: A 160 LEU cc_start: 0.7090 (tm) cc_final: 0.6015 (mt) REVERT: A 544 MET cc_start: 0.7929 (ttt) cc_final: 0.7722 (ttp) REVERT: A 610 ASN cc_start: 0.8220 (t0) cc_final: 0.7851 (t0) outliers start: 8 outliers final: 0 residues processed: 104 average time/residue: 1.0558 time to fit residues: 115.6048 Evaluate side-chains 92 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 66 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 67 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 ASN B 112 ASN B 547 GLN A 68 ASN A 547 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6018 Z= 0.224 Angle : 0.543 5.804 8200 Z= 0.283 Chirality : 0.039 0.147 990 Planarity : 0.004 0.040 990 Dihedral : 4.104 15.780 800 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 2.66 % Allowed : 14.26 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.31), residues: 746 helix: 1.71 (0.22), residues: 560 sheet: 2.20 (0.85), residues: 42 loop : -1.15 (0.52), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 506 HIS 0.001 0.001 HIS A 187 PHE 0.011 0.002 PHE B 603 TYR 0.006 0.001 TYR B 635 ARG 0.002 0.000 ARG B 493 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 102 time to evaluate : 0.653 Fit side-chains REVERT: B 160 LEU cc_start: 0.7151 (tm) cc_final: 0.6051 (mt) REVERT: B 472 ASN cc_start: 0.5008 (t0) cc_final: 0.4494 (t0) REVERT: B 610 ASN cc_start: 0.8214 (t0) cc_final: 0.7807 (t0) REVERT: A 160 LEU cc_start: 0.7142 (tm) cc_final: 0.6005 (mt) REVERT: A 472 ASN cc_start: 0.5050 (t0) cc_final: 0.4541 (t0) REVERT: A 610 ASN cc_start: 0.8224 (t0) cc_final: 0.7828 (t0) outliers start: 17 outliers final: 6 residues processed: 115 average time/residue: 1.1177 time to fit residues: 134.9032 Evaluate side-chains 102 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 96 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 201 LYS Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 568 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 59 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 1 optimal weight: 0.9980 chunk 53 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 ASN B 547 GLN A 68 ASN A 547 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6018 Z= 0.242 Angle : 0.550 5.755 8200 Z= 0.289 Chirality : 0.039 0.151 990 Planarity : 0.004 0.041 990 Dihedral : 4.176 15.695 800 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 2.66 % Allowed : 15.05 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.31), residues: 746 helix: 1.63 (0.22), residues: 556 sheet: 2.08 (0.86), residues: 42 loop : -1.21 (0.49), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 506 HIS 0.001 0.001 HIS A 187 PHE 0.012 0.002 PHE B 603 TYR 0.006 0.001 TYR A 635 ARG 0.002 0.000 ARG B 207 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 105 time to evaluate : 0.670 Fit side-chains REVERT: B 160 LEU cc_start: 0.7179 (tm) cc_final: 0.6065 (mt) REVERT: B 472 ASN cc_start: 0.5040 (t0) cc_final: 0.4548 (t0) REVERT: B 610 ASN cc_start: 0.8203 (t0) cc_final: 0.7813 (t0) REVERT: A 176 LYS cc_start: 0.7157 (mmtt) cc_final: 0.6454 (ttpp) REVERT: A 472 ASN cc_start: 0.5046 (t0) cc_final: 0.4554 (t0) REVERT: A 610 ASN cc_start: 0.8218 (t0) cc_final: 0.7828 (t0) outliers start: 17 outliers final: 9 residues processed: 116 average time/residue: 1.0157 time to fit residues: 124.2340 Evaluate side-chains 107 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 98 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 201 LYS Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 568 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 24 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 17 optimal weight: 8.9990 chunk 71 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 ASN A 68 ASN A 112 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6018 Z= 0.173 Angle : 0.523 7.254 8200 Z= 0.273 Chirality : 0.037 0.136 990 Planarity : 0.004 0.039 990 Dihedral : 4.122 15.658 800 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 2.19 % Allowed : 15.52 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.31), residues: 746 helix: 1.72 (0.22), residues: 556 sheet: 2.10 (0.87), residues: 42 loop : -1.17 (0.50), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 506 HIS 0.001 0.000 HIS B 187 PHE 0.014 0.001 PHE B 603 TYR 0.006 0.001 TYR B 8 ARG 0.001 0.000 ARG A 512 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 104 time to evaluate : 0.683 Fit side-chains REVERT: B 472 ASN cc_start: 0.5115 (t0) cc_final: 0.4643 (t0) REVERT: B 610 ASN cc_start: 0.8206 (t0) cc_final: 0.7800 (t0) REVERT: A 160 LEU cc_start: 0.7108 (tm) cc_final: 0.6000 (mt) REVERT: A 472 ASN cc_start: 0.5092 (t0) cc_final: 0.4626 (t0) REVERT: A 610 ASN cc_start: 0.8201 (t0) cc_final: 0.7798 (t0) outliers start: 14 outliers final: 7 residues processed: 112 average time/residue: 1.0021 time to fit residues: 118.4123 Evaluate side-chains 105 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 98 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 568 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 69 optimal weight: 2.9990 chunk 8 optimal weight: 9.9990 chunk 40 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 ASN A 68 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6018 Z= 0.206 Angle : 0.539 7.593 8200 Z= 0.282 Chirality : 0.038 0.142 990 Planarity : 0.004 0.040 990 Dihedral : 4.139 15.729 800 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 2.04 % Allowed : 17.55 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.31), residues: 746 helix: 1.69 (0.22), residues: 556 sheet: 2.04 (0.87), residues: 42 loop : -1.23 (0.50), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 506 HIS 0.001 0.000 HIS B 187 PHE 0.015 0.001 PHE B 603 TYR 0.006 0.001 TYR A 8 ARG 0.001 0.000 ARG B 512 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 101 time to evaluate : 0.684 Fit side-chains REVERT: B 160 LEU cc_start: 0.7172 (tm) cc_final: 0.6095 (mt) REVERT: B 472 ASN cc_start: 0.5148 (t0) cc_final: 0.4745 (t0) REVERT: B 610 ASN cc_start: 0.8219 (t0) cc_final: 0.7797 (t0) REVERT: A 472 ASN cc_start: 0.5155 (t0) cc_final: 0.4756 (t0) REVERT: A 610 ASN cc_start: 0.8221 (t0) cc_final: 0.7804 (t0) outliers start: 13 outliers final: 6 residues processed: 110 average time/residue: 0.9765 time to fit residues: 113.8105 Evaluate side-chains 103 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 97 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 568 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 42 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 45 optimal weight: 10.0000 chunk 48 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 ASN A 68 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6018 Z= 0.226 Angle : 0.570 7.055 8200 Z= 0.295 Chirality : 0.039 0.147 990 Planarity : 0.004 0.040 990 Dihedral : 4.197 15.773 800 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 1.88 % Allowed : 18.34 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.31), residues: 746 helix: 1.62 (0.22), residues: 556 sheet: 1.98 (0.86), residues: 42 loop : -1.23 (0.49), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 506 HIS 0.001 0.000 HIS B 187 PHE 0.017 0.002 PHE A 622 TYR 0.006 0.001 TYR A 635 ARG 0.001 0.000 ARG B 512 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 95 time to evaluate : 0.635 Fit side-chains REVERT: B 160 LEU cc_start: 0.7197 (tm) cc_final: 0.6102 (mt) REVERT: B 472 ASN cc_start: 0.5145 (t0) cc_final: 0.4769 (t0) REVERT: B 610 ASN cc_start: 0.8215 (t0) cc_final: 0.7814 (t0) REVERT: A 472 ASN cc_start: 0.5164 (t0) cc_final: 0.4790 (t0) REVERT: A 610 ASN cc_start: 0.8213 (t0) cc_final: 0.7815 (t0) outliers start: 12 outliers final: 4 residues processed: 104 average time/residue: 0.8647 time to fit residues: 95.6700 Evaluate side-chains 99 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 95 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 568 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 28 optimal weight: 0.0570 chunk 52 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 ASN A 68 ASN A 494 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 6018 Z= 0.158 Angle : 0.538 7.192 8200 Z= 0.276 Chirality : 0.037 0.125 990 Planarity : 0.004 0.039 990 Dihedral : 4.106 15.477 800 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 0.94 % Allowed : 20.22 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.31), residues: 746 helix: 1.75 (0.22), residues: 560 sheet: 2.01 (0.86), residues: 42 loop : -1.23 (0.52), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 506 HIS 0.001 0.000 HIS B 5 PHE 0.015 0.001 PHE B 603 TYR 0.006 0.001 TYR A 635 ARG 0.001 0.000 ARG B 512 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 99 time to evaluate : 0.670 Fit side-chains REVERT: B 160 LEU cc_start: 0.7048 (tm) cc_final: 0.5991 (mt) REVERT: B 472 ASN cc_start: 0.5233 (t0) cc_final: 0.4849 (t0) REVERT: B 610 ASN cc_start: 0.8207 (t0) cc_final: 0.7782 (t0) REVERT: A 176 LYS cc_start: 0.7270 (mmtt) cc_final: 0.6585 (ttpp) REVERT: A 472 ASN cc_start: 0.5252 (t0) cc_final: 0.4868 (t0) REVERT: A 610 ASN cc_start: 0.8203 (t0) cc_final: 0.7780 (t0) outliers start: 6 outliers final: 0 residues processed: 103 average time/residue: 0.9335 time to fit residues: 102.1934 Evaluate side-chains 93 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 33 optimal weight: 0.0970 chunk 48 optimal weight: 0.3980 chunk 73 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 chunk 46 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 ASN A 68 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6018 Z= 0.160 Angle : 0.550 7.221 8200 Z= 0.283 Chirality : 0.038 0.149 990 Planarity : 0.004 0.036 990 Dihedral : 4.073 15.102 800 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 0.47 % Allowed : 21.79 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.31), residues: 746 helix: 1.69 (0.22), residues: 562 sheet: 1.94 (0.85), residues: 42 loop : -1.17 (0.52), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 506 HIS 0.001 0.000 HIS B 5 PHE 0.026 0.001 PHE A 622 TYR 0.005 0.001 TYR A 635 ARG 0.001 0.000 ARG B 512 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 91 time to evaluate : 0.668 Fit side-chains REVERT: B 37 ASP cc_start: 0.5321 (p0) cc_final: 0.5033 (t0) REVERT: B 160 LEU cc_start: 0.7046 (tm) cc_final: 0.5960 (mt) REVERT: B 472 ASN cc_start: 0.5205 (t0) cc_final: 0.4859 (t0) REVERT: B 610 ASN cc_start: 0.8195 (t0) cc_final: 0.7788 (t0) REVERT: A 37 ASP cc_start: 0.5321 (p0) cc_final: 0.5031 (t0) REVERT: A 176 LYS cc_start: 0.7245 (mmtt) cc_final: 0.6560 (ttpp) REVERT: A 472 ASN cc_start: 0.5206 (t0) cc_final: 0.4855 (t0) REVERT: A 610 ASN cc_start: 0.8190 (t0) cc_final: 0.7791 (t0) outliers start: 3 outliers final: 0 residues processed: 93 average time/residue: 0.8919 time to fit residues: 88.0475 Evaluate side-chains 91 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 54 optimal weight: 0.7980 chunk 8 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 51 optimal weight: 0.2980 chunk 3 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 ASN A 68 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.159390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.127563 restraints weight = 7221.808| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.65 r_work: 0.3346 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 6018 Z= 0.184 Angle : 0.561 7.980 8200 Z= 0.288 Chirality : 0.039 0.149 990 Planarity : 0.004 0.038 990 Dihedral : 4.079 15.329 800 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 0.94 % Allowed : 20.85 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.31), residues: 746 helix: 1.65 (0.22), residues: 560 sheet: 1.96 (0.84), residues: 42 loop : -1.22 (0.52), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 506 HIS 0.001 0.000 HIS B 203 PHE 0.021 0.001 PHE B 603 TYR 0.006 0.001 TYR A 8 ARG 0.001 0.000 ARG A 512 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2377.03 seconds wall clock time: 42 minutes 45.44 seconds (2565.44 seconds total)