Starting phenix.real_space_refine on Thu Dec 7 16:37:30 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ag3_15414/12_2023/8ag3_15414.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ag3_15414/12_2023/8ag3_15414.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ag3_15414/12_2023/8ag3_15414.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ag3_15414/12_2023/8ag3_15414.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ag3_15414/12_2023/8ag3_15414.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ag3_15414/12_2023/8ag3_15414.pdb" } resolution = 3.47 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= 0.001 sd= 0.015 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 20 5.16 5 C 1668 2.51 5 N 436 2.21 5 O 508 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 44": "OE1" <-> "OE2" Residue "C PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 2632 Number of models: 1 Model: "" Number of chains: 2 Chain: "C" Number of atoms: 1316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1316 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 5, 'TRANS': 155} Chain: "D" Number of atoms: 1316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1316 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 5, 'TRANS': 155} Time building chain proxies: 1.94, per 1000 atoms: 0.74 Number of scatterers: 2632 At special positions: 0 Unit cell: (78.49, 64.295, 64.295, 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 20 16.00 O 508 8.00 N 436 7.00 C 1668 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: 1.15 Conformation dependent library (CDL) restraints added in 665.6 milliseconds 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 624 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 4 sheets defined 16.1% alpha, 52.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'C' and resid 20 through 31 removed outlier: 3.778A pdb=" N ASN C 24 " --> pdb=" O ASP C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 60 Processing helix chain 'D' and resid 22 through 31 Processing helix chain 'D' and resid 46 through 61 removed outlier: 4.125A pdb=" N ILE D 50 " --> pdb=" O ASN D 46 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 38 through 42 removed outlier: 7.238A pdb=" N THR C 72 " --> pdb=" O ASP C 155 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ASP C 155 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS C 149 " --> pdb=" O TYR C 78 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N THR C 150 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N THR C 11 " --> pdb=" O ALA C 134 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE D 3 " --> pdb=" O THR D 11 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N THR D 11 " --> pdb=" O ALA D 134 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP D 130 " --> pdb=" O PHE D 15 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU D 103 " --> pdb=" O LEU D 154 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N THR D 150 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LYS D 149 " --> pdb=" O TYR D 78 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 64 through 69 removed outlier: 3.619A pdb=" N CYS C 66 " --> pdb=" O SER C 159 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N THR C 150 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N THR C 11 " --> pdb=" O ALA C 134 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE D 3 " --> pdb=" O THR D 11 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N THR D 11 " --> pdb=" O ALA D 134 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP D 130 " --> pdb=" O PHE D 15 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU D 103 " --> pdb=" O LEU D 154 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N THR D 150 " --> pdb=" O LEU D 107 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 85 through 86 removed outlier: 3.897A pdb=" N PHE C 139 " --> pdb=" O ARG C 86 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASP C 138 " --> pdb=" O TYR C 119 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER C 127 " --> pdb=" O ILE C 116 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 112 through 113 removed outlier: 6.831A pdb=" N CYS D 112 " --> pdb=" O LEU D 145 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU D 145 " --> pdb=" O CYS D 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 150 hydrogen bonds defined for protein. 423 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.64 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 852 1.35 - 1.46: 557 1.46 - 1.58: 1237 1.58 - 1.69: 0 1.69 - 1.81: 30 Bond restraints: 2676 Sorted by residual: bond pdb=" CB GLU C 65 " pdb=" CG GLU C 65 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.24e+00 bond pdb=" CB PRO C 80 " pdb=" CG PRO C 80 " ideal model delta sigma weight residual 1.492 1.540 -0.048 5.00e-02 4.00e+02 9.38e-01 bond pdb=" CA GLU C 65 " pdb=" CB GLU C 65 " ideal model delta sigma weight residual 1.534 1.546 -0.013 1.45e-02 4.76e+03 7.44e-01 bond pdb=" CB MET D 43 " pdb=" CG MET D 43 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 7.20e-01 bond pdb=" CA LYS D 7 " pdb=" CB LYS D 7 " ideal model delta sigma weight residual 1.530 1.541 -0.011 1.68e-02 3.54e+03 4.56e-01 ... (remaining 2671 not shown) Histogram of bond angle deviations from ideal: 98.95 - 105.95: 42 105.95 - 112.94: 1478 112.94 - 119.94: 864 119.94 - 126.94: 1210 126.94 - 133.94: 16 Bond angle restraints: 3610 Sorted by residual: angle pdb=" CA GLU C 65 " pdb=" CB GLU C 65 " pdb=" CG GLU C 65 " ideal model delta sigma weight residual 114.10 121.07 -6.97 2.00e+00 2.50e-01 1.22e+01 angle pdb=" CA MET D 43 " pdb=" CB MET D 43 " pdb=" CG MET D 43 " ideal model delta sigma weight residual 114.10 120.97 -6.87 2.00e+00 2.50e-01 1.18e+01 angle pdb=" CB MET D 43 " pdb=" CG MET D 43 " pdb=" SD MET D 43 " ideal model delta sigma weight residual 112.70 121.58 -8.88 3.00e+00 1.11e-01 8.77e+00 angle pdb=" CA PRO C 80 " pdb=" N PRO C 80 " pdb=" CD PRO C 80 " ideal model delta sigma weight residual 112.00 108.65 3.35 1.40e+00 5.10e-01 5.73e+00 angle pdb=" C MET D 43 " pdb=" CA MET D 43 " pdb=" CB MET D 43 " ideal model delta sigma weight residual 110.19 114.05 -3.86 1.62e+00 3.81e-01 5.66e+00 ... (remaining 3605 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.04: 1299 13.04 - 26.08: 225 26.08 - 39.11: 81 39.11 - 52.15: 37 52.15 - 65.19: 12 Dihedral angle restraints: 1654 sinusoidal: 694 harmonic: 960 Sorted by residual: dihedral pdb=" CA ASP C 128 " pdb=" CB ASP C 128 " pdb=" CG ASP C 128 " pdb=" OD1 ASP C 128 " ideal model delta sinusoidal sigma weight residual -30.00 -89.18 59.18 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CA ASP C 83 " pdb=" CB ASP C 83 " pdb=" CG ASP C 83 " pdb=" OD1 ASP C 83 " ideal model delta sinusoidal sigma weight residual -30.00 -87.13 57.13 1 2.00e+01 2.50e-03 1.10e+01 dihedral pdb=" CA LYS D 77 " pdb=" CB LYS D 77 " pdb=" CG LYS D 77 " pdb=" CD LYS D 77 " ideal model delta sinusoidal sigma weight residual 60.00 117.48 -57.48 3 1.50e+01 4.44e-03 9.44e+00 ... (remaining 1651 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 238 0.028 - 0.057: 103 0.057 - 0.085: 37 0.085 - 0.113: 28 0.113 - 0.141: 6 Chirality restraints: 412 Sorted by residual: chirality pdb=" CA ILE C 73 " pdb=" N ILE C 73 " pdb=" C ILE C 73 " pdb=" CB ILE C 73 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.99e-01 chirality pdb=" CA ILE C 105 " pdb=" N ILE C 105 " pdb=" C ILE C 105 " pdb=" CB ILE C 105 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.91e-01 chirality pdb=" CB ILE D 39 " pdb=" CA ILE D 39 " pdb=" CG1 ILE D 39 " pdb=" CG2 ILE D 39 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.14 2.00e-01 2.50e+01 4.68e-01 ... (remaining 409 not shown) Planarity restraints: 458 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 79 " -0.088 5.00e-02 4.00e+02 1.33e-01 2.81e+01 pdb=" N PRO C 80 " 0.229 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " -0.072 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS C 120 " 0.037 5.00e-02 4.00e+02 5.67e-02 5.14e+00 pdb=" N PRO C 121 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO C 121 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 121 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET D 43 " -0.005 2.00e-02 2.50e+03 9.79e-03 9.58e-01 pdb=" C MET D 43 " 0.017 2.00e-02 2.50e+03 pdb=" O MET D 43 " -0.007 2.00e-02 2.50e+03 pdb=" N GLU D 44 " -0.006 2.00e-02 2.50e+03 ... (remaining 455 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 59 2.69 - 3.25: 2329 3.25 - 3.80: 3801 3.80 - 4.35: 5021 4.35 - 4.90: 8610 Nonbonded interactions: 19820 Sorted by model distance: nonbonded pdb=" O ASP C 48 " pdb=" ND2 ASN C 52 " model vdw 2.143 2.520 nonbonded pdb=" O GLN C 10 " pdb=" OH TYR C 101 " model vdw 2.232 2.440 nonbonded pdb=" O GLN D 10 " pdb=" OH TYR D 101 " model vdw 2.294 2.440 nonbonded pdb=" N GLU C 44 " pdb=" OE1 GLU C 44 " model vdw 2.344 2.520 nonbonded pdb=" NH1 ARG D 23 " pdb=" O TYR D 106 " model vdw 2.350 2.520 ... (remaining 19815 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 'C' selection = chain 'D' } 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: 1.400 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: 5.580 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.460 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 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 0.048 2676 Z= 0.167 Angle : 0.600 8.883 3610 Z= 0.322 Chirality : 0.044 0.141 412 Planarity : 0.007 0.133 458 Dihedral : 17.158 65.191 1030 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 0.00 % Allowed : 34.74 % Favored : 65.26 % 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: -1.45 (0.47), residues: 318 helix: 2.05 (0.79), residues: 50 sheet: -0.29 (0.51), residues: 112 loop : -2.61 (0.43), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 91 HIS 0.002 0.001 HIS C 32 PHE 0.010 0.001 PHE D 15 TYR 0.009 0.001 TYR D 4 ARG 0.001 0.000 ARG D 27 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 0.264 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.1747 time to fit residues: 20.8397 Evaluate side-chains 105 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.313 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 27 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 25 optimal weight: 0.0870 chunk 9 optimal weight: 0.0980 chunk 15 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 52 ASN ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.0911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2676 Z= 0.216 Angle : 0.546 5.850 3610 Z= 0.294 Chirality : 0.044 0.142 412 Planarity : 0.006 0.099 458 Dihedral : 4.488 12.470 350 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 1.95 % Allowed : 30.84 % Favored : 67.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.48), residues: 318 helix: 2.02 (0.79), residues: 50 sheet: 0.01 (0.54), residues: 102 loop : -2.46 (0.44), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP D 91 HIS 0.003 0.001 HIS C 120 PHE 0.012 0.001 PHE C 133 TYR 0.011 0.002 TYR D 101 ARG 0.001 0.000 ARG D 27 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 106 time to evaluate : 0.305 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 107 average time/residue: 0.1674 time to fit residues: 20.7237 Evaluate side-chains 111 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 107 time to evaluate : 0.316 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0293 time to fit residues: 0.6610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 16 optimal weight: 0.9990 chunk 9 optimal weight: 0.4980 chunk 24 optimal weight: 0.0030 chunk 19 optimal weight: 0.3980 chunk 8 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.2980 chunk 28 optimal weight: 0.4980 chunk 23 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 overall best weight: 0.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 52 ASN ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2676 Z= 0.177 Angle : 0.509 4.817 3610 Z= 0.278 Chirality : 0.044 0.166 412 Planarity : 0.005 0.086 458 Dihedral : 4.370 11.602 350 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 2.60 % Allowed : 28.90 % Favored : 68.51 % 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: -1.17 (0.48), residues: 318 helix: 2.17 (0.79), residues: 50 sheet: 0.09 (0.53), residues: 102 loop : -2.42 (0.44), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 91 HIS 0.002 0.001 HIS C 120 PHE 0.012 0.001 PHE C 133 TYR 0.010 0.001 TYR D 101 ARG 0.003 0.000 ARG C 60 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 105 time to evaluate : 0.318 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 111 average time/residue: 0.1641 time to fit residues: 21.1203 Evaluate side-chains 113 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 109 time to evaluate : 0.315 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0293 time to fit residues: 0.6608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 15 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 30 optimal weight: 0.0970 chunk 27 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 52 ASN D 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 2676 Z= 0.312 Angle : 0.582 7.945 3610 Z= 0.315 Chirality : 0.045 0.156 412 Planarity : 0.005 0.083 458 Dihedral : 4.713 12.315 350 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer: Outliers : 4.55 % Allowed : 26.30 % Favored : 69.16 % 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: -1.28 (0.47), residues: 318 helix: 1.89 (0.78), residues: 50 sheet: 0.09 (0.53), residues: 102 loop : -2.49 (0.44), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 91 HIS 0.003 0.001 HIS C 120 PHE 0.015 0.002 PHE C 133 TYR 0.012 0.002 TYR D 101 ARG 0.006 0.000 ARG C 60 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 110 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 10 residues processed: 115 average time/residue: 0.1640 time to fit residues: 21.7178 Evaluate side-chains 121 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 111 time to evaluate : 0.291 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0818 time to fit residues: 1.4553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 23 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 10 GLN C 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 2676 Z= 0.315 Angle : 0.599 8.642 3610 Z= 0.322 Chirality : 0.046 0.167 412 Planarity : 0.005 0.081 458 Dihedral : 4.763 13.384 350 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 1.30 % Allowed : 29.87 % Favored : 68.83 % 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 (0.47), residues: 318 helix: 1.73 (0.77), residues: 50 sheet: 0.00 (0.52), residues: 102 loop : -2.52 (0.43), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP D 91 HIS 0.003 0.001 HIS C 120 PHE 0.016 0.002 PHE C 133 TYR 0.013 0.002 TYR D 101 ARG 0.005 0.000 ARG C 60 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 110 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 112 average time/residue: 0.1759 time to fit residues: 22.6680 Evaluate side-chains 113 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 111 time to evaluate : 0.311 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0386 time to fit residues: 0.5745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 0.0870 chunk 25 optimal weight: 0.0980 chunk 14 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 chunk 3 optimal weight: 0.2980 chunk 17 optimal weight: 0.4980 chunk 22 optimal weight: 0.9990 overall best weight: 0.3158 ------------------------------------------------------------------------------- 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: 0.7049 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2676 Z= 0.181 Angle : 0.560 8.371 3610 Z= 0.297 Chirality : 0.044 0.148 412 Planarity : 0.005 0.078 458 Dihedral : 4.481 12.212 350 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 1.62 % Allowed : 30.52 % Favored : 67.86 % 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: -1.19 (0.46), residues: 318 helix: 2.11 (0.79), residues: 50 sheet: 0.57 (0.61), residues: 78 loop : -2.38 (0.39), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP D 91 HIS 0.001 0.001 HIS C 120 PHE 0.013 0.001 PHE C 133 TYR 0.010 0.001 TYR D 101 ARG 0.003 0.000 ARG C 60 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 110 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 111 average time/residue: 0.1658 time to fit residues: 21.2980 Evaluate side-chains 113 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 110 time to evaluate : 0.314 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0292 time to fit residues: 0.6166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 17 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 30 optimal weight: 0.0980 chunk 19 optimal weight: 4.9990 chunk 18 optimal weight: 0.0050 chunk 14 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 overall best weight: 0.3994 ------------------------------------------------------------------------------- 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: 0.7052 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2676 Z= 0.204 Angle : 0.578 8.406 3610 Z= 0.301 Chirality : 0.045 0.186 412 Planarity : 0.005 0.077 458 Dihedral : 4.485 13.438 350 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 0.65 % Allowed : 33.12 % Favored : 66.23 % 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: -1.11 (0.47), residues: 318 helix: 2.10 (0.78), residues: 50 sheet: 0.77 (0.61), residues: 78 loop : -2.38 (0.40), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP D 91 HIS 0.002 0.001 HIS C 120 PHE 0.013 0.001 PHE C 133 TYR 0.014 0.002 TYR D 119 ARG 0.003 0.000 ARG C 60 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 105 time to evaluate : 0.340 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 107 average time/residue: 0.1706 time to fit residues: 21.1316 Evaluate side-chains 103 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 102 time to evaluate : 0.335 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0299 time to fit residues: 0.5095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 15 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 8 optimal weight: 0.0570 chunk 25 optimal weight: 0.9980 overall best weight: 0.5098 ------------------------------------------------------------------------------- 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: 0.7059 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 2676 Z= 0.250 Angle : 0.582 9.219 3610 Z= 0.307 Chirality : 0.046 0.200 412 Planarity : 0.005 0.077 458 Dihedral : 4.606 13.593 350 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 1.95 % Allowed : 31.17 % Favored : 66.88 % 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: -1.16 (0.48), residues: 318 helix: 1.97 (0.78), residues: 50 sheet: 0.20 (0.53), residues: 102 loop : -2.43 (0.44), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 91 HIS 0.002 0.001 HIS C 120 PHE 0.014 0.001 PHE C 133 TYR 0.012 0.002 TYR D 119 ARG 0.005 0.000 ARG C 60 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 110 time to evaluate : 0.329 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 111 average time/residue: 0.1681 time to fit residues: 21.4502 Evaluate side-chains 113 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 110 time to evaluate : 0.309 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0291 time to fit residues: 0.6007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 27 optimal weight: 0.0980 chunk 28 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.7071 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 2676 Z= 0.302 Angle : 0.612 9.886 3610 Z= 0.324 Chirality : 0.047 0.192 412 Planarity : 0.005 0.078 458 Dihedral : 4.761 14.050 350 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 0.65 % Allowed : 33.44 % Favored : 65.91 % 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: -1.29 (0.47), residues: 318 helix: 1.85 (0.78), residues: 50 sheet: 0.08 (0.53), residues: 102 loop : -2.47 (0.44), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 91 HIS 0.003 0.001 HIS C 120 PHE 0.016 0.002 PHE C 133 TYR 0.015 0.002 TYR D 119 ARG 0.002 0.000 ARG C 60 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 110 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 110 average time/residue: 0.1761 time to fit residues: 22.2351 Evaluate side-chains 110 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 0.319 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 15 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 25 optimal weight: 0.0000 chunk 10 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 4 optimal weight: 0.0980 chunk 22 optimal weight: 0.0670 overall best weight: 0.2722 ------------------------------------------------------------------------------- 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: 0.7038 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 2676 Z= 0.181 Angle : 0.583 10.174 3610 Z= 0.304 Chirality : 0.047 0.220 412 Planarity : 0.005 0.077 458 Dihedral : 4.518 17.050 350 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 0.32 % Allowed : 34.09 % Favored : 65.58 % 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: -1.18 (0.48), residues: 318 helix: 2.13 (0.80), residues: 50 sheet: 0.09 (0.52), residues: 102 loop : -2.42 (0.44), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP D 91 HIS 0.002 0.001 HIS C 120 PHE 0.012 0.001 PHE C 133 TYR 0.011 0.001 TYR D 119 ARG 0.004 0.000 ARG C 60 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 107 time to evaluate : 0.319 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 107 average time/residue: 0.1724 time to fit residues: 21.2300 Evaluate side-chains 107 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 0.281 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 1 optimal weight: 0.3980 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 21 optimal weight: 0.3980 chunk 0 optimal weight: 0.1980 chunk 20 optimal weight: 0.9990 chunk 19 optimal weight: 0.0570 chunk 12 optimal weight: 0.8980 chunk 11 optimal weight: 0.3980 chunk 31 optimal weight: 1.9990 overall best weight: 0.2898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.136417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.112657 restraints weight = 3611.895| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.56 r_work: 0.3227 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2676 Z= 0.190 Angle : 0.605 10.004 3610 Z= 0.309 Chirality : 0.047 0.208 412 Planarity : 0.005 0.076 458 Dihedral : 4.491 18.792 350 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 1.30 % Allowed : 33.77 % Favored : 64.94 % 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: -1.10 (0.48), residues: 318 helix: 2.28 (0.79), residues: 50 sheet: 0.12 (0.53), residues: 102 loop : -2.39 (0.45), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP D 91 HIS 0.002 0.001 HIS C 120 PHE 0.012 0.001 PHE C 133 TYR 0.009 0.001 TYR D 101 ARG 0.005 0.000 ARG C 60 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1271.29 seconds wall clock time: 23 minutes 35.15 seconds (1415.15 seconds total)