Starting phenix.real_space_refine (version: dev) on Tue Nov 29 12:58:59 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kjr_22898/11_2022/7kjr_22898_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kjr_22898/11_2022/7kjr_22898.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kjr_22898/11_2022/7kjr_22898.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kjr_22898/11_2022/7kjr_22898.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kjr_22898/11_2022/7kjr_22898_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kjr_22898/11_2022/7kjr_22898_updated.pdb" } resolution = 2.08 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.067 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 3840 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1575 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 4, 'TRANS': 188} Chain breaks: 1 Chain: "B" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1575 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 4, 'TRANS': 188} Chain breaks: 1 Chain: "C" Number of atoms: 261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 261 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 1, 'TRANS': 29} Chain: "D" Number of atoms: 261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 261 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 1, 'TRANS': 29} Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 28 Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 28 Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 61 Classifications: {'water': 61} Link IDs: {None: 60} Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 61 Classifications: {'water': 61} Link IDs: {None: 60} Time building chain proxies: 2.83, per 1000 atoms: 0.74 Number of scatterers: 3840 At special positions: 0 Unit cell: (77.789, 67.611, 90.148, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 18 16.00 P 2 15.00 O 794 8.00 N 580 7.00 C 2446 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: 1.70 Conformation dependent library (CDL) restraints added in 666.0 milliseconds 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 848 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 13 helices and 2 sheets defined 53.3% alpha, 18.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 43 through 62 removed outlier: 3.535A pdb=" N GLN A 57 " --> pdb=" O ALA A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 99 Processing helix chain 'A' and resid 103 through 133 removed outlier: 5.545A pdb=" N TYR A 107 " --> pdb=" O PRO A 104 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA A 110 " --> pdb=" O TYR A 107 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N CYS A 133 " --> pdb=" O CYS A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 140 No H-bonds generated for 'chain 'A' and resid 137 through 140' Processing helix chain 'A' and resid 220 through 223 No H-bonds generated for 'chain 'A' and resid 220 through 223' Processing helix chain 'B' and resid 43 through 62 removed outlier: 3.538A pdb=" N GLN B 57 " --> pdb=" O ALA B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 99 Processing helix chain 'B' and resid 103 through 133 removed outlier: 4.673A pdb=" N TYR B 107 " --> pdb=" O ALA B 103 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N LEU B 108 " --> pdb=" O PRO B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 140 No H-bonds generated for 'chain 'B' and resid 137 through 140' Processing helix chain 'B' and resid 220 through 223 No H-bonds generated for 'chain 'B' and resid 220 through 223' Processing helix chain 'C' and resid 26 through 54 Proline residue: C 34 - end of helix removed outlier: 5.027A pdb=" N GLY C 49 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N LEU C 50 " --> pdb=" O GLU C 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 46 Proline residue: D 34 - end of helix Processing helix chain 'D' and resid 48 through 54 Processing sheet with id= A, first strand: chain 'A' and resid 155 through 160 removed outlier: 5.965A pdb=" N HIS A 150 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N CYS A 200 " --> pdb=" O HIS A 150 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ILE A 232 " --> pdb=" O TYR A 215 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N THR A 217 " --> pdb=" O PHE A 230 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N PHE A 230 " --> pdb=" O THR A 217 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 155 through 160 removed outlier: 5.963A pdb=" N HIS B 150 " --> pdb=" O CYS B 200 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N CYS B 200 " --> pdb=" O HIS B 150 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ILE B 232 " --> pdb=" O TYR B 215 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N THR B 217 " --> pdb=" O PHE B 230 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N PHE B 230 " --> pdb=" O THR B 217 " (cutoff:3.500A) 237 hydrogen bonds defined for protein. 522 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: 1.21 Time building geometry restraints manager: 1.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 857 1.33 - 1.45: 906 1.45 - 1.57: 2029 1.57 - 1.69: 2 1.69 - 1.81: 24 Bond restraints: 3818 Sorted by residual: bond pdb=" O4P PEE B 301 " pdb=" P PEE B 301 " ideal model delta sigma weight residual 1.653 1.769 -0.116 2.00e-02 2.50e+03 3.37e+01 bond pdb=" O4P PEE A 301 " pdb=" P PEE A 301 " ideal model delta sigma weight residual 1.653 1.769 -0.116 2.00e-02 2.50e+03 3.37e+01 bond pdb=" C4 PEE A 301 " pdb=" O4P PEE A 301 " ideal model delta sigma weight residual 1.409 1.365 0.044 2.00e-02 2.50e+03 4.76e+00 bond pdb=" C4 PEE B 301 " pdb=" O4P PEE B 301 " ideal model delta sigma weight residual 1.409 1.366 0.043 2.00e-02 2.50e+03 4.70e+00 bond pdb=" C ILE B 62 " pdb=" O ILE B 62 " ideal model delta sigma weight residual 1.236 1.218 0.018 1.19e-02 7.06e+03 2.25e+00 ... (remaining 3813 not shown) Histogram of bond angle deviations from ideal: 99.97 - 106.79: 72 106.79 - 113.61: 2087 113.61 - 120.43: 1478 120.43 - 127.24: 1499 127.24 - 134.06: 50 Bond angle restraints: 5186 Sorted by residual: angle pdb=" CB GLN C 37 " pdb=" CG GLN C 37 " pdb=" CD GLN C 37 " ideal model delta sigma weight residual 112.60 118.61 -6.01 1.70e+00 3.46e-01 1.25e+01 angle pdb=" CB GLU B 226 " pdb=" CG GLU B 226 " pdb=" CD GLU B 226 " ideal model delta sigma weight residual 112.60 118.44 -5.84 1.70e+00 3.46e-01 1.18e+01 angle pdb=" O1P PEE A 301 " pdb=" P PEE A 301 " pdb=" O4P PEE A 301 " ideal model delta sigma weight residual 109.92 99.97 9.95 3.00e+00 1.11e-01 1.10e+01 angle pdb=" O1P PEE B 301 " pdb=" P PEE B 301 " pdb=" O4P PEE B 301 " ideal model delta sigma weight residual 109.92 99.99 9.93 3.00e+00 1.11e-01 1.09e+01 angle pdb=" O1P PEE A 301 " pdb=" P PEE A 301 " pdb=" O2P PEE A 301 " ideal model delta sigma weight residual 119.43 129.00 -9.57 3.00e+00 1.11e-01 1.02e+01 ... (remaining 5181 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.49: 1993 20.49 - 40.98: 126 40.98 - 61.46: 42 61.46 - 81.95: 5 81.95 - 102.44: 4 Dihedral angle restraints: 2170 sinusoidal: 848 harmonic: 1322 Sorted by residual: dihedral pdb=" C32 PEE A 301 " pdb=" C30 PEE A 301 " pdb=" C31 PEE A 301 " pdb=" O3 PEE A 301 " ideal model delta sinusoidal sigma weight residual 161.16 -96.40 -102.44 1 3.00e+01 1.11e-03 1.30e+01 dihedral pdb=" CA HIS B 204 " pdb=" C HIS B 204 " pdb=" N SER B 205 " pdb=" CA SER B 205 " ideal model delta harmonic sigma weight residual 180.00 162.84 17.16 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA HIS A 204 " pdb=" C HIS A 204 " pdb=" N SER A 205 " pdb=" CA SER A 205 " ideal model delta harmonic sigma weight residual 180.00 163.80 16.20 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 2167 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 352 0.036 - 0.071: 156 0.071 - 0.107: 47 0.107 - 0.142: 15 0.142 - 0.178: 6 Chirality restraints: 576 Sorted by residual: chirality pdb=" CG LEU A 147 " pdb=" CB LEU A 147 " pdb=" CD1 LEU A 147 " pdb=" CD2 LEU A 147 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.88e-01 chirality pdb=" CG LEU B 147 " pdb=" CB LEU B 147 " pdb=" CD1 LEU B 147 " pdb=" CD2 LEU B 147 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.81e-01 chirality pdb=" CG LEU A 101 " pdb=" CB LEU A 101 " pdb=" CD1 LEU A 101 " pdb=" CD2 LEU A 101 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.68e-01 ... (remaining 573 not shown) Planarity restraints: 626 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR B 113 " 0.011 2.00e-02 2.50e+03 2.30e-02 5.27e+00 pdb=" C TYR B 113 " -0.040 2.00e-02 2.50e+03 pdb=" O TYR B 113 " 0.015 2.00e-02 2.50e+03 pdb=" N PHE B 114 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN D 37 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.15e+00 pdb=" CD GLN D 37 " 0.039 2.00e-02 2.50e+03 pdb=" OE1 GLN D 37 " -0.015 2.00e-02 2.50e+03 pdb=" NE2 GLN D 37 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 114 " 0.010 2.00e-02 2.50e+03 1.95e-02 3.82e+00 pdb=" C PHE B 114 " -0.034 2.00e-02 2.50e+03 pdb=" O PHE B 114 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU B 115 " 0.011 2.00e-02 2.50e+03 ... (remaining 623 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 920 2.78 - 3.31: 3603 3.31 - 3.84: 7359 3.84 - 4.37: 8455 4.37 - 4.90: 13685 Nonbonded interactions: 34022 Sorted by model distance: nonbonded pdb=" O HOH A 424 " pdb=" O HOH A 451 " model vdw 2.254 2.440 nonbonded pdb=" O HOH B 401 " pdb=" O HOH B 433 " model vdw 2.274 2.440 nonbonded pdb=" OG SER A 216 " pdb=" OE1 GLN A 218 " model vdw 2.274 2.440 nonbonded pdb=" OG SER B 216 " pdb=" OE1 GLN B 218 " model vdw 2.276 2.440 nonbonded pdb=" O HOH A 401 " pdb=" O HOH A 437 " model vdw 2.294 2.440 ... (remaining 34017 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' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 18 5.16 5 C 2446 2.51 5 N 580 2.21 5 O 794 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 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: 5.640 Check model and map are aligned: 0.060 Convert atoms to be neutral: 0.030 Process input model: 17.300 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:12.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 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 : 0.006 0.116 3818 Z= 0.390 Angle : 0.843 9.946 5186 Z= 0.426 Chirality : 0.047 0.178 576 Planarity : 0.005 0.036 626 Dihedral : 16.311 102.441 1322 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer Outliers : 0.25 % 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: 1.13 (0.37), residues: 436 helix: 1.81 (0.31), residues: 234 sheet: 0.02 (0.48), residues: 90 loop : -0.81 (0.53), residues: 112 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 68 time to evaluate : 0.461 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 69 average time/residue: 1.1807 time to fit residues: 84.2912 Evaluate side-chains 67 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 66 time to evaluate : 0.474 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.6372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 37 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 11 optimal weight: 0.4980 chunk 22 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 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 144 ASN C 42 ASN D 42 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.0781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.022 3818 Z= 0.211 Angle : 0.527 7.206 5186 Z= 0.291 Chirality : 0.040 0.132 576 Planarity : 0.005 0.030 626 Dihedral : 8.298 72.368 502 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer Outliers : 2.22 % 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: 1.40 (0.37), residues: 436 helix: 2.08 (0.31), residues: 234 sheet: 0.27 (0.47), residues: 86 loop : -0.91 (0.51), residues: 116 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 69 time to evaluate : 0.471 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 73 average time/residue: 1.1793 time to fit residues: 89.0704 Evaluate side-chains 73 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 68 time to evaluate : 0.476 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 2 residues processed: 3 average time/residue: 0.5711 time to fit residues: 2.4262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 22 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 11 optimal weight: 0.0670 chunk 40 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 42 ASN D 42 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.020 3818 Z= 0.188 Angle : 0.488 6.816 5186 Z= 0.269 Chirality : 0.039 0.133 576 Planarity : 0.005 0.028 626 Dihedral : 7.688 64.832 502 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer Outliers : 1.48 % 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: 1.36 (0.37), residues: 436 helix: 2.01 (0.32), residues: 234 sheet: 0.24 (0.46), residues: 86 loop : -0.82 (0.53), residues: 116 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 70 time to evaluate : 0.414 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 72 average time/residue: 1.1677 time to fit residues: 87.0644 Evaluate side-chains 74 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 69 time to evaluate : 0.537 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 2 residues processed: 3 average time/residue: 0.5610 time to fit residues: 2.3762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 39 optimal weight: 0.9990 chunk 30 optimal weight: 0.0970 chunk 20 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 40 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 11 optimal weight: 0.2980 chunk 35 optimal weight: 3.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 42 ASN D 42 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.018 3818 Z= 0.160 Angle : 0.466 6.113 5186 Z= 0.257 Chirality : 0.039 0.134 576 Planarity : 0.004 0.028 626 Dihedral : 7.461 68.435 502 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer Outliers : 1.72 % 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: 1.39 (0.38), residues: 436 helix: 2.02 (0.32), residues: 234 sheet: 0.28 (0.47), residues: 86 loop : -0.82 (0.54), residues: 116 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 68 time to evaluate : 0.469 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 71 average time/residue: 1.1345 time to fit residues: 83.3735 Evaluate side-chains 73 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 68 time to evaluate : 0.432 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 2 residues processed: 3 average time/residue: 0.5472 time to fit residues: 2.3397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 0.0570 chunk 36 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 10 optimal weight: 0.3980 chunk 14 optimal weight: 1.9990 chunk 8 optimal weight: 0.3980 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 42 ASN D 42 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.018 3818 Z= 0.147 Angle : 0.456 5.705 5186 Z= 0.250 Chirality : 0.038 0.134 576 Planarity : 0.004 0.028 626 Dihedral : 7.287 71.567 502 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer Outliers : 0.99 % 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: 1.47 (0.38), residues: 436 helix: 2.10 (0.32), residues: 234 sheet: 0.30 (0.46), residues: 86 loop : -0.81 (0.54), residues: 116 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 69 time to evaluate : 0.458 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 71 average time/residue: 1.2066 time to fit residues: 88.6483 Evaluate side-chains 72 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 68 time to evaluate : 0.424 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 0.0392 time to fit residues: 0.7357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 41 optimal weight: 6.9990 chunk 4 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 42 ASN D 42 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.020 3818 Z= 0.187 Angle : 0.487 6.723 5186 Z= 0.265 Chirality : 0.039 0.134 576 Planarity : 0.004 0.027 626 Dihedral : 7.497 73.179 502 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer Outliers : 1.48 % 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: 1.40 (0.38), residues: 436 helix: 2.00 (0.32), residues: 234 sheet: 0.35 (0.47), residues: 86 loop : -0.80 (0.53), residues: 116 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 68 time to evaluate : 0.474 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 70 average time/residue: 1.1880 time to fit residues: 86.0366 Evaluate side-chains 73 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 68 time to evaluate : 0.473 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 2 residues processed: 3 average time/residue: 0.6242 time to fit residues: 2.5977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 28 optimal weight: 0.0370 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 42 ASN D 42 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.018 3818 Z= 0.162 Angle : 0.471 6.103 5186 Z= 0.257 Chirality : 0.039 0.135 576 Planarity : 0.004 0.027 626 Dihedral : 7.421 75.594 502 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer Outliers : 0.99 % 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: 1.43 (0.38), residues: 436 helix: 2.05 (0.33), residues: 234 sheet: 0.29 (0.47), residues: 86 loop : -0.80 (0.53), residues: 116 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 69 time to evaluate : 0.468 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 71 average time/residue: 1.2031 time to fit residues: 88.2772 Evaluate side-chains 73 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 69 time to evaluate : 0.476 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 0.0375 time to fit residues: 0.7624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 20 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 42 ASN D 42 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.028 3818 Z= 0.282 Angle : 0.559 8.314 5186 Z= 0.299 Chirality : 0.042 0.167 576 Planarity : 0.005 0.027 626 Dihedral : 8.000 74.378 502 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer Outliers : 1.23 % 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: 1.27 (0.38), residues: 436 helix: 1.94 (0.32), residues: 234 sheet: 0.03 (0.48), residues: 90 loop : -0.72 (0.55), residues: 112 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 67 time to evaluate : 0.351 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 69 average time/residue: 1.2206 time to fit residues: 86.9486 Evaluate side-chains 71 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 67 time to evaluate : 0.472 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 0.8825 time to fit residues: 2.4289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 35 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 25 optimal weight: 0.0370 chunk 41 optimal weight: 8.9990 chunk 19 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 34 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 42 ASN D 42 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.021 3818 Z= 0.194 Angle : 0.511 6.902 5186 Z= 0.276 Chirality : 0.040 0.132 576 Planarity : 0.005 0.027 626 Dihedral : 7.780 76.984 502 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer Outliers : 0.74 % 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: 1.35 (0.38), residues: 436 helix: 1.97 (0.32), residues: 234 sheet: 0.32 (0.47), residues: 86 loop : -0.84 (0.53), residues: 116 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 68 time to evaluate : 0.483 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 70 average time/residue: 1.1900 time to fit residues: 86.1519 Evaluate side-chains 71 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 68 time to evaluate : 0.476 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 0.0367 time to fit residues: 0.6752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 26 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 42 ASN D 42 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 3818 Z= 0.198 Angle : 0.522 6.917 5186 Z= 0.282 Chirality : 0.040 0.132 576 Planarity : 0.005 0.026 626 Dihedral : 7.780 79.714 502 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer Outliers : 0.49 % 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: 1.35 (0.38), residues: 436 helix: 1.96 (0.32), residues: 234 sheet: 0.31 (0.47), residues: 86 loop : -0.83 (0.54), residues: 116 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 67 time to evaluate : 0.447 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 69 average time/residue: 1.2344 time to fit residues: 88.0610 Evaluate side-chains 69 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 67 time to evaluate : 0.490 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.6234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 4 optimal weight: 0.6980 chunk 6 optimal weight: 0.0670 chunk 30 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 17 optimal weight: 0.0270 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 42 ASN D 42 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.134423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.098172 restraints weight = 3506.870| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.60 r_work: 0.3130 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 1.42 restraints_weight: 0.2500 r_work: 0.3098 rms_B_bonded: 1.49 restraints_weight: 0.1250 r_work: 0.3080 rms_B_bonded: 1.61 restraints_weight: 0.0625 r_work: 0.3062 rms_B_bonded: 1.77 restraints_weight: 0.0312 r_work: 0.3043 rms_B_bonded: 1.98 restraints_weight: 0.0156 r_work: 0.3022 rms_B_bonded: 2.24 restraints_weight: 0.0078 r_work: 0.3000 rms_B_bonded: 2.55 restraints_weight: 0.0039 r_work: 0.2976 rms_B_bonded: 2.91 restraints_weight: 0.0020 r_work: 0.2950 rms_B_bonded: 3.34 restraints_weight: 0.0010 r_work: 0.2922 rms_B_bonded: 3.84 restraints_weight: 0.0005 r_work: 0.2892 rms_B_bonded: 4.42 restraints_weight: 0.0002 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 3818 Z= 0.159 Angle : 0.502 5.802 5186 Z= 0.272 Chirality : 0.039 0.134 576 Planarity : 0.004 0.026 626 Dihedral : 7.583 84.704 502 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer Outliers : 0.74 % 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: 1.37 (0.38), residues: 436 helix: 2.01 (0.33), residues: 234 sheet: 0.27 (0.46), residues: 86 loop : -0.83 (0.53), residues: 116 =============================================================================== Job complete usr+sys time: 1930.03 seconds wall clock time: 35 minutes 22.81 seconds (2122.81 seconds total)