Starting phenix.real_space_refine (version: 1.21rc1) on Mon Jul 3 22:05:51 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sza_40905/07_2023/8sza_40905_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sza_40905/07_2023/8sza_40905.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sza_40905/07_2023/8sza_40905.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sza_40905/07_2023/8sza_40905.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sza_40905/07_2023/8sza_40905_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sza_40905/07_2023/8sza_40905_updated.pdb" } resolution = 2.75 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= 0.001 sd= 0.025 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 12 5.16 5 C 3258 2.51 5 N 726 2.21 5 O 804 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 69": "OE1" <-> "OE2" Residue "A PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 116": "OD1" <-> "OD2" Residue "C TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 49": "OE1" <-> "OE2" Residue "D ASP 53": "OD1" <-> "OD2" Residue "E ASP 53": "OD1" <-> "OD2" Residue "E PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 49": "OE1" <-> "OE2" Residue "F ASP 53": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 4800 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 772 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "B" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 772 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "C" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 772 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "D" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 772 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "E" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 772 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "F" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 772 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.81, per 1000 atoms: 0.59 Number of scatterers: 4800 At special positions: 0 Unit cell: (56.76, 70.62, 94.38, 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 12 16.00 O 804 8.00 N 726 7.00 C 3258 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.23 Conformation dependent library (CDL) restraints added in 708.5 milliseconds 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1164 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 0 sheets defined 82.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 40 through 51 removed outlier: 3.965A pdb=" N MET A 51 " --> pdb=" O ALA A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 70 Processing helix chain 'A' and resid 77 through 107 removed outlier: 4.120A pdb=" N LYS A 103 " --> pdb=" O ILE A 99 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N TYR A 104 " --> pdb=" O PHE A 100 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU A 106 " --> pdb=" O VAL A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 138 Processing helix chain 'B' and resid 40 through 51 removed outlier: 3.953A pdb=" N MET B 51 " --> pdb=" O ALA B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 70 Processing helix chain 'B' and resid 77 through 106 removed outlier: 4.175A pdb=" N LYS B 103 " --> pdb=" O ILE B 99 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N TYR B 104 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP B 105 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU B 106 " --> pdb=" O VAL B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 138 Processing helix chain 'C' and resid 40 through 51 removed outlier: 3.506A pdb=" N SER C 50 " --> pdb=" O SER C 46 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N MET C 51 " --> pdb=" O ALA C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 70 Processing helix chain 'C' and resid 77 through 99 Processing helix chain 'C' and resid 112 through 138 Processing helix chain 'D' and resid 40 through 51 removed outlier: 4.065A pdb=" N MET D 51 " --> pdb=" O ALA D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 70 Processing helix chain 'D' and resid 77 through 106 removed outlier: 3.512A pdb=" N VAL D 102 " --> pdb=" O LEU D 98 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LYS D 103 " --> pdb=" O ILE D 99 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N TYR D 104 " --> pdb=" O PHE D 100 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU D 106 " --> pdb=" O VAL D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 138 removed outlier: 3.643A pdb=" N PHE D 135 " --> pdb=" O VAL D 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 51 removed outlier: 4.013A pdb=" N MET E 51 " --> pdb=" O ALA E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 70 Processing helix chain 'E' and resid 77 through 102 Processing helix chain 'E' and resid 104 through 107 No H-bonds generated for 'chain 'E' and resid 104 through 107' Processing helix chain 'E' and resid 112 through 138 Processing helix chain 'F' and resid 40 through 51 removed outlier: 4.272A pdb=" N MET F 51 " --> pdb=" O ALA F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 70 Processing helix chain 'F' and resid 77 through 102 Processing helix chain 'F' and resid 112 through 138 381 hydrogen bonds defined for protein. 1143 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: 1.29 Time building geometry restraints manager: 2.40 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: 1416 1.35 - 1.46: 1057 1.46 - 1.58: 2405 1.58 - 1.70: 0 1.70 - 1.82: 24 Bond restraints: 4902 Sorted by residual: bond pdb=" CB GLU A 69 " pdb=" CG GLU A 69 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.06e+00 bond pdb=" CA PHE C 74 " pdb=" CB PHE C 74 " ideal model delta sigma weight residual 1.528 1.507 0.021 1.58e-02 4.01e+03 1.70e+00 bond pdb=" CD2 HIS F 112 " pdb=" NE2 HIS F 112 " ideal model delta sigma weight residual 1.374 1.360 0.014 1.10e-02 8.26e+03 1.61e+00 bond pdb=" CA HIS F 112 " pdb=" CB HIS F 112 " ideal model delta sigma weight residual 1.528 1.510 0.019 1.59e-02 3.96e+03 1.39e+00 bond pdb=" CG HIS F 112 " pdb=" ND1 HIS F 112 " ideal model delta sigma weight residual 1.378 1.390 -0.012 1.10e-02 8.26e+03 1.28e+00 ... (remaining 4897 not shown) Histogram of bond angle deviations from ideal: 99.31 - 105.72: 97 105.72 - 112.14: 2731 112.14 - 118.55: 1316 118.55 - 124.97: 2528 124.97 - 131.39: 36 Bond angle restraints: 6708 Sorted by residual: angle pdb=" CB MET A 51 " pdb=" CG MET A 51 " pdb=" SD MET A 51 " ideal model delta sigma weight residual 112.70 123.47 -10.77 3.00e+00 1.11e-01 1.29e+01 angle pdb=" CA MET A 58 " pdb=" CB MET A 58 " pdb=" CG MET A 58 " ideal model delta sigma weight residual 114.10 120.87 -6.77 2.00e+00 2.50e-01 1.14e+01 angle pdb=" CA GLU A 69 " pdb=" CB GLU A 69 " pdb=" CG GLU A 69 " ideal model delta sigma weight residual 114.10 120.83 -6.73 2.00e+00 2.50e-01 1.13e+01 angle pdb=" C TYR D 77 " pdb=" N VAL D 78 " pdb=" CA VAL D 78 " ideal model delta sigma weight residual 120.33 122.84 -2.51 8.00e-01 1.56e+00 9.83e+00 angle pdb=" CB GLU A 69 " pdb=" CG GLU A 69 " pdb=" CD GLU A 69 " ideal model delta sigma weight residual 112.60 117.81 -5.21 1.70e+00 3.46e-01 9.41e+00 ... (remaining 6703 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.55: 2496 16.55 - 33.09: 280 33.09 - 49.64: 65 49.64 - 66.19: 14 66.19 - 82.73: 1 Dihedral angle restraints: 2856 sinusoidal: 1074 harmonic: 1782 Sorted by residual: dihedral pdb=" CG LYS B 65 " pdb=" CD LYS B 65 " pdb=" CE LYS B 65 " pdb=" NZ LYS B 65 " ideal model delta sinusoidal sigma weight residual -60.00 -2.88 -57.12 3 1.50e+01 4.44e-03 9.43e+00 dihedral pdb=" CG LYS B 103 " pdb=" CD LYS B 103 " pdb=" CE LYS B 103 " pdb=" NZ LYS B 103 " ideal model delta sinusoidal sigma weight residual 180.00 122.94 57.06 3 1.50e+01 4.44e-03 9.43e+00 dihedral pdb=" N MET E 51 " pdb=" CA MET E 51 " pdb=" CB MET E 51 " pdb=" CG MET E 51 " ideal model delta sinusoidal sigma weight residual -180.00 -123.30 -56.70 3 1.50e+01 4.44e-03 9.41e+00 ... (remaining 2853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.021: 454 0.021 - 0.042: 244 0.042 - 0.063: 109 0.063 - 0.084: 45 0.084 - 0.104: 18 Chirality restraints: 870 Sorted by residual: chirality pdb=" CB VAL A 67 " pdb=" CA VAL A 67 " pdb=" CG1 VAL A 67 " pdb=" CG2 VAL A 67 " both_signs ideal model delta sigma weight residual False -2.63 -2.52 -0.10 2.00e-01 2.50e+01 2.73e-01 chirality pdb=" CA PRO F 79 " pdb=" N PRO F 79 " pdb=" C PRO F 79 " pdb=" CB PRO F 79 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.48e-01 chirality pdb=" CA PRO C 79 " pdb=" N PRO C 79 " pdb=" C PRO C 79 " pdb=" CB PRO C 79 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.42e-01 ... (remaining 867 not shown) Planarity restraints: 780 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 127 " -0.013 2.00e-02 2.50e+03 1.72e-02 5.18e+00 pdb=" CG PHE A 127 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE A 127 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A 127 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE A 127 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 127 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 127 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 69 " -0.010 2.00e-02 2.50e+03 2.12e-02 4.50e+00 pdb=" CD GLU A 69 " 0.037 2.00e-02 2.50e+03 pdb=" OE1 GLU A 69 " -0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU A 69 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP F 53 " -0.006 2.00e-02 2.50e+03 1.29e-02 1.66e+00 pdb=" CG ASP F 53 " 0.022 2.00e-02 2.50e+03 pdb=" OD1 ASP F 53 " -0.008 2.00e-02 2.50e+03 pdb=" OD2 ASP F 53 " -0.008 2.00e-02 2.50e+03 ... (remaining 777 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 184 2.73 - 3.27: 5230 3.27 - 3.81: 7815 3.81 - 4.36: 8986 4.36 - 4.90: 15080 Nonbonded interactions: 37295 Sorted by model distance: nonbonded pdb=" O MET D 58 " pdb=" OG SER D 62 " model vdw 2.185 2.440 nonbonded pdb=" OH TYR F 104 " pdb=" O1 CLR F 201 " model vdw 2.196 2.440 nonbonded pdb=" O MET E 58 " pdb=" OG SER E 62 " model vdw 2.225 2.440 nonbonded pdb=" OD1 ASN D 120 " pdb=" NZ LYS E 103 " model vdw 2.351 2.520 nonbonded pdb=" O MET F 58 " pdb=" OG SER F 62 " model vdw 2.414 2.440 ... (remaining 37290 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' and resid 39 through 139) selection = (chain 'C' and resid 39 through 139) selection = (chain 'D' and resid 39 through 139) selection = (chain 'E' and resid 39 through 139) selection = (chain 'F' and resid 39 through 139) } 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: 3.690 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: 0.010 Extract box with map and model: 9.820 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 16.870 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 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 : 0.003 0.043 4902 Z= 0.211 Angle : 0.652 10.766 6708 Z= 0.325 Chirality : 0.033 0.104 870 Planarity : 0.002 0.022 780 Dihedral : 14.831 82.732 1692 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Rotamer Outliers : 0.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.35), residues: 594 helix: 1.96 (0.23), residues: 492 sheet: None (None), residues: 0 loop : -1.39 (0.67), residues: 102 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 87 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 90 average time/residue: 0.7758 time to fit residues: 74.0836 Evaluate side-chains 89 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 84 time to evaluate : 0.502 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 4 residues processed: 2 average time/residue: 0.0894 time to fit residues: 0.9101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 30 optimal weight: 8.9990 chunk 24 optimal weight: 0.9980 chunk 47 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 54 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 4902 Z= 0.193 Angle : 0.546 7.019 6708 Z= 0.274 Chirality : 0.035 0.139 870 Planarity : 0.003 0.016 780 Dihedral : 4.225 33.021 672 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer Outliers : 2.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.89 (0.35), residues: 594 helix: 2.51 (0.23), residues: 492 sheet: None (None), residues: 0 loop : -1.23 (0.69), residues: 102 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 92 time to evaluate : 0.580 Fit side-chains outliers start: 14 outliers final: 8 residues processed: 100 average time/residue: 0.7046 time to fit residues: 75.0729 Evaluate side-chains 91 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 83 time to evaluate : 0.513 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 5 residues processed: 3 average time/residue: 0.0781 time to fit residues: 1.0036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 4902 Z= 0.196 Angle : 0.541 6.866 6708 Z= 0.264 Chirality : 0.036 0.118 870 Planarity : 0.002 0.016 780 Dihedral : 4.326 32.544 672 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 3.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.36), residues: 594 helix: 2.02 (0.23), residues: 534 sheet: None (None), residues: 0 loop : -2.51 (0.82), residues: 60 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 90 time to evaluate : 0.542 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 13 residues processed: 100 average time/residue: 0.7020 time to fit residues: 74.7311 Evaluate side-chains 95 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 82 time to evaluate : 0.499 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 7 residues processed: 6 average time/residue: 0.0616 time to fit residues: 1.2972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 0.4980 chunk 28 optimal weight: 3.9990 chunk 6 optimal weight: 0.0970 chunk 26 optimal weight: 1.9990 chunk 36 optimal weight: 0.3980 chunk 54 optimal weight: 0.7980 chunk 57 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 32 optimal weight: 0.2980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 4902 Z= 0.153 Angle : 0.522 7.268 6708 Z= 0.253 Chirality : 0.034 0.107 870 Planarity : 0.002 0.017 780 Dihedral : 4.069 31.800 672 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Rotamer Outliers : 3.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.69 (0.36), residues: 594 helix: 2.22 (0.23), residues: 528 sheet: None (None), residues: 0 loop : -1.99 (0.78), residues: 66 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 94 time to evaluate : 0.561 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 9 residues processed: 108 average time/residue: 0.6495 time to fit residues: 75.0069 Evaluate side-chains 94 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 85 time to evaluate : 0.542 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 8 residues processed: 1 average time/residue: 0.0917 time to fit residues: 0.8332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 49 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 29 optimal weight: 0.3980 chunk 52 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 11 optimal weight: 0.0040 chunk 34 optimal weight: 0.9980 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 ASN E 63 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 4902 Z= 0.163 Angle : 0.559 12.523 6708 Z= 0.266 Chirality : 0.035 0.103 870 Planarity : 0.002 0.015 780 Dihedral : 3.976 31.180 672 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 3.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.70 (0.36), residues: 594 helix: 2.20 (0.23), residues: 534 sheet: None (None), residues: 0 loop : -2.20 (0.87), residues: 60 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 92 time to evaluate : 0.561 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 13 residues processed: 106 average time/residue: 0.6384 time to fit residues: 72.4996 Evaluate side-chains 98 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 85 time to evaluate : 0.556 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 10 residues processed: 3 average time/residue: 0.0837 time to fit residues: 1.1252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 7.9990 chunk 55 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 ASN ** C 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 4902 Z= 0.190 Angle : 0.568 7.763 6708 Z= 0.274 Chirality : 0.035 0.103 870 Planarity : 0.002 0.018 780 Dihedral : 4.043 30.985 672 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Rotamer Outliers : 3.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.67 (0.36), residues: 594 helix: 2.18 (0.23), residues: 528 sheet: None (None), residues: 0 loop : -1.71 (0.83), residues: 66 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 91 time to evaluate : 0.510 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 12 residues processed: 101 average time/residue: 0.6510 time to fit residues: 70.3166 Evaluate side-chains 99 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 87 time to evaluate : 0.570 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 9 residues processed: 4 average time/residue: 0.0695 time to fit residues: 1.1769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 57 optimal weight: 0.4980 chunk 36 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 4902 Z= 0.199 Angle : 0.581 8.202 6708 Z= 0.284 Chirality : 0.036 0.104 870 Planarity : 0.002 0.015 780 Dihedral : 4.096 30.766 672 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Rotamer Outliers : 3.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.59 (0.36), residues: 594 helix: 2.14 (0.23), residues: 528 sheet: None (None), residues: 0 loop : -1.91 (0.81), residues: 66 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 89 time to evaluate : 0.527 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 8 residues processed: 101 average time/residue: 0.6251 time to fit residues: 67.8811 Evaluate side-chains 94 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 86 time to evaluate : 0.593 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 7 residues processed: 1 average time/residue: 0.0944 time to fit residues: 0.8713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 50 optimal weight: 0.0070 chunk 53 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 16 optimal weight: 0.2980 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 4902 Z= 0.167 Angle : 0.587 10.382 6708 Z= 0.280 Chirality : 0.034 0.105 870 Planarity : 0.002 0.018 780 Dihedral : 3.880 29.966 672 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Rotamer Outliers : 1.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.80 (0.36), residues: 594 helix: 2.37 (0.23), residues: 522 sheet: None (None), residues: 0 loop : -2.24 (0.74), residues: 72 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 97 time to evaluate : 0.515 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 10 residues processed: 105 average time/residue: 0.6565 time to fit residues: 73.7592 Evaluate side-chains 96 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 86 time to evaluate : 0.527 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 8 residues processed: 2 average time/residue: 0.0857 time to fit residues: 1.1512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 56 optimal weight: 0.2980 chunk 34 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 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 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 4902 Z= 0.198 Angle : 0.582 8.150 6708 Z= 0.289 Chirality : 0.035 0.116 870 Planarity : 0.002 0.020 780 Dihedral : 3.964 29.864 672 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Rotamer Outliers : 2.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.66 (0.35), residues: 594 helix: 2.26 (0.23), residues: 522 sheet: None (None), residues: 0 loop : -2.19 (0.73), residues: 72 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 88 time to evaluate : 0.551 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 10 residues processed: 97 average time/residue: 0.6562 time to fit residues: 68.1951 Evaluate side-chains 93 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 83 time to evaluate : 0.497 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 8 residues processed: 2 average time/residue: 0.0680 time to fit residues: 0.8605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 37 optimal weight: 0.0050 chunk 50 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 43 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 ASN F 107 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 4902 Z= 0.186 Angle : 0.607 9.052 6708 Z= 0.295 Chirality : 0.035 0.129 870 Planarity : 0.002 0.023 780 Dihedral : 3.871 29.349 672 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer Outliers : 2.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.73 (0.35), residues: 594 helix: 2.31 (0.23), residues: 522 sheet: None (None), residues: 0 loop : -2.18 (0.72), residues: 72 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 88 time to evaluate : 0.553 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 9 residues processed: 97 average time/residue: 0.6279 time to fit residues: 65.2710 Evaluate side-chains 93 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 84 time to evaluate : 0.516 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 8 residues processed: 1 average time/residue: 0.0933 time to fit residues: 0.7863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 54 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.189525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.158979 restraints weight = 6409.156| |-----------------------------------------------------------------------------| r_work (start): 0.4264 rms_B_bonded: 2.46 r_work: 0.4152 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.4152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 4902 Z= 0.206 Angle : 0.597 8.511 6708 Z= 0.296 Chirality : 0.036 0.125 870 Planarity : 0.002 0.021 780 Dihedral : 3.946 29.400 672 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer Outliers : 2.16 % 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: 2.68 (0.35), residues: 594 helix: 2.27 (0.23), residues: 522 sheet: None (None), residues: 0 loop : -2.13 (0.73), residues: 72 =============================================================================== Job complete usr+sys time: 1831.46 seconds wall clock time: 33 minutes 14.28 seconds (1994.28 seconds total)