Starting phenix.real_space_refine on Mon Nov 13 22:25:18 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wks_32568/11_2023/7wks_32568.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wks_32568/11_2023/7wks_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_32568/11_2023/7wks_32568.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wks_32568/11_2023/7wks_32568.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wks_32568/11_2023/7wks_32568.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wks_32568/11_2023/7wks_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-1.21rc1-5144/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: 3.72, 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: 2.36 Conformation dependent library (CDL) restraints added in 1.3 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: 0.53 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: 1.60 Time building geometry restraints manager: 2.50 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: 0.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 3.310 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 19.990 Find NCS groups from input model: 0.270 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:11.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.200 ------------------------------------------------------------------------------- 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 *********************** 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 : 0.692 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 1.1663 time to fit residues: 137.9163 Evaluate side-chains 95 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.678 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9454 ------------------------------------------------------------------------------- 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: 0.6980 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: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.0831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6018 Z= 0.169 Angle : 0.521 6.301 8200 Z= 0.267 Chirality : 0.037 0.132 990 Planarity : 0.004 0.038 990 Dihedral : 4.086 15.127 800 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 0.78 % Allowed : 11.13 % Favored : 88.09 % 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: 1.97 (0.31), residues: 746 helix: 1.81 (0.22), residues: 564 sheet: 2.03 (0.84), residues: 42 loop : -0.97 (0.54), residues: 140 *********************** 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 105 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 100 time to evaluate : 0.686 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 102 average time/residue: 1.1085 time to fit residues: 118.9206 Evaluate side-chains 88 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 87 time to evaluate : 0.659 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 1.2242 time to fit residues: 2.2151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 55 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 112 ASN A 472 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1201 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= 0.220 Angle : 0.538 6.845 8200 Z= 0.278 Chirality : 0.038 0.144 990 Planarity : 0.004 0.040 990 Dihedral : 4.122 15.599 800 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.57 % Allowed : 13.95 % Favored : 84.48 % 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: 1.70 (0.21), residues: 562 sheet: 2.09 (0.84), residues: 42 loop : -1.08 (0.52), residues: 142 *********************** 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 109 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 99 time to evaluate : 0.655 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 109 average time/residue: 1.1029 time to fit residues: 126.4499 Evaluate side-chains 96 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 92 time to evaluate : 0.615 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 0.8926 ------------------------------------------------------------------------------- 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: 5.9990 chunk 50 optimal weight: 4.9990 chunk 34 optimal weight: 0.0470 chunk 7 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 64 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.8280 ------------------------------------------------------------------------------- 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: 0.7966 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6018 Z= 0.155 Angle : 0.506 6.465 8200 Z= 0.261 Chirality : 0.037 0.128 990 Planarity : 0.004 0.038 990 Dihedral : 4.055 15.481 800 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 2.04 % Allowed : 14.73 % Favored : 83.23 % 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: 1.95 (0.31), residues: 746 helix: 1.84 (0.22), residues: 560 sheet: 2.01 (0.83), residues: 42 loop : -1.14 (0.51), residues: 144 *********************** 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 110 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 97 time to evaluate : 0.618 Fit side-chains outliers start: 13 outliers final: 5 residues processed: 109 average time/residue: 1.0750 time to fit residues: 123.7466 Evaluate side-chains 98 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 93 time to evaluate : 0.693 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 4 residues processed: 1 average time/residue: 0.2061 time to fit residues: 1.1855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 59 optimal weight: 0.3980 chunk 40 optimal weight: 0.3980 chunk 1 optimal weight: 0.9990 chunk 53 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 18 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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: 0.7944 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 6018 Z= 0.141 Angle : 0.500 6.393 8200 Z= 0.257 Chirality : 0.036 0.129 990 Planarity : 0.004 0.036 990 Dihedral : 3.984 15.182 800 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 1.72 % Allowed : 15.67 % Favored : 82.60 % 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: 2.09 (0.31), residues: 746 helix: 1.94 (0.22), residues: 558 sheet: 2.00 (0.84), residues: 42 loop : -1.00 (0.51), residues: 146 *********************** 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 111 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 100 time to evaluate : 0.641 Fit side-chains outliers start: 11 outliers final: 4 residues processed: 108 average time/residue: 1.0372 time to fit residues: 118.0645 Evaluate side-chains 94 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 90 time to evaluate : 0.710 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.0521 time to fit residues: 0.9980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 24 optimal weight: 0.7980 chunk 64 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 17 optimal weight: 0.2980 chunk 71 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 ASN B 612 HIS A 68 ASN A 612 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6018 Z= 0.146 Angle : 0.507 6.366 8200 Z= 0.260 Chirality : 0.037 0.135 990 Planarity : 0.004 0.037 990 Dihedral : 3.965 15.100 800 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 2.04 % Allowed : 17.08 % Favored : 80.88 % 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: 2.07 (0.31), residues: 746 helix: 1.92 (0.22), residues: 558 sheet: 2.03 (0.84), residues: 42 loop : -0.98 (0.52), residues: 146 *********************** 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 107 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 94 time to evaluate : 0.697 Fit side-chains outliers start: 13 outliers final: 5 residues processed: 104 average time/residue: 1.0192 time to fit residues: 111.8769 Evaluate side-chains 94 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 89 time to evaluate : 0.706 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 2 average time/residue: 0.2009 time to fit residues: 1.4608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 69 optimal weight: 0.9980 chunk 8 optimal weight: 9.9990 chunk 40 optimal weight: 0.9980 chunk 52 optimal weight: 8.9990 chunk 60 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 71 optimal weight: 0.4980 chunk 44 optimal weight: 5.9990 chunk 43 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 612 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 6018 Z= 0.155 Angle : 0.517 6.522 8200 Z= 0.267 Chirality : 0.037 0.127 990 Planarity : 0.004 0.038 990 Dihedral : 3.969 15.123 800 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 1.72 % Allowed : 17.40 % Favored : 80.88 % 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: 2.05 (0.31), residues: 746 helix: 1.89 (0.22), residues: 558 sheet: 2.11 (0.85), residues: 42 loop : -0.96 (0.52), residues: 146 *********************** 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 107 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 96 time to evaluate : 0.697 Fit side-chains outliers start: 11 outliers final: 1 residues processed: 105 average time/residue: 1.0400 time to fit residues: 114.9525 Evaluate side-chains 92 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 91 time to evaluate : 0.672 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.9112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 14 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 45 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 56 optimal weight: 8.9990 chunk 64 optimal weight: 0.6980 chunk 68 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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: 0.7965 moved from start: 0.1601 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= 0.181 Angle : 0.535 7.022 8200 Z= 0.276 Chirality : 0.038 0.133 990 Planarity : 0.004 0.039 990 Dihedral : 4.034 15.164 800 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 1.41 % Allowed : 18.81 % 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: 1.95 (0.31), residues: 746 helix: 1.84 (0.22), residues: 556 sheet: 2.01 (0.84), residues: 42 loop : -1.03 (0.52), residues: 148 *********************** 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 101 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 92 time to evaluate : 0.679 Fit side-chains outliers start: 9 outliers final: 1 residues processed: 101 average time/residue: 1.0058 time to fit residues: 107.4049 Evaluate side-chains 92 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 91 time to evaluate : 0.647 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.8411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 68 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 28 optimal weight: 0.0980 chunk 52 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 70 optimal weight: 0.0870 chunk 42 optimal weight: 0.9990 overall best weight: 1.0362 ------------------------------------------------------------------------------- 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: 0.7965 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 0.050 6018 Z= 0.182 Angle : 0.546 7.530 8200 Z= 0.282 Chirality : 0.038 0.137 990 Planarity : 0.004 0.039 990 Dihedral : 4.063 15.188 800 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 0.63 % Allowed : 19.75 % Favored : 79.62 % 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: 1.84 (0.31), residues: 746 helix: 1.77 (0.22), residues: 556 sheet: 1.97 (0.83), residues: 42 loop : -1.11 (0.52), residues: 148 *********************** 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 97 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 93 time to evaluate : 0.708 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 97 average time/residue: 1.0374 time to fit residues: 106.3384 Evaluate side-chains 91 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 90 time to evaluate : 0.717 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.9636 ------------------------------------------------------------------------------- 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: 0.0370 chunk 48 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 chunk 35 optimal weight: 0.6980 chunk 46 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 17 optimal weight: 0.5980 overall best weight: 0.6058 ------------------------------------------------------------------------------- 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: 0.7940 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 6018 Z= 0.156 Angle : 0.539 7.468 8200 Z= 0.279 Chirality : 0.038 0.143 990 Planarity : 0.004 0.036 990 Dihedral : 4.052 15.059 800 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 0.78 % Allowed : 19.59 % Favored : 79.62 % 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: 1.83 (0.31), residues: 746 helix: 1.74 (0.22), residues: 562 sheet: 1.92 (0.82), residues: 42 loop : -1.13 (0.54), residues: 142 ********************** 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: 5 poor density : 89 time to evaluate : 0.704 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 94 average time/residue: 0.9812 time to fit residues: 97.6189 Evaluate side-chains 88 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 87 time to evaluate : 0.621 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.8803 ------------------------------------------------------------------------------- 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: 0.0000 chunk 8 optimal weight: 10.0000 chunk 16 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 overall best weight: 0.6184 ------------------------------------------------------------------------------- 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 = 0.3899 r_free = 0.3899 target = 0.164044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.131130 restraints weight = 6982.371| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 1.68 r_work: 0.3399 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 6018 Z= 0.152 Angle : 0.533 8.084 8200 Z= 0.274 Chirality : 0.038 0.145 990 Planarity : 0.004 0.038 990 Dihedral : 4.028 14.989 800 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 0.47 % Allowed : 20.38 % Favored : 79.15 % 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: 1.85 (0.31), residues: 746 helix: 1.77 (0.22), residues: 562 sheet: 1.80 (0.82), residues: 42 loop : -1.15 (0.53), residues: 142 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2428.88 seconds wall clock time: 43 minutes 43.55 seconds (2623.55 seconds total)