Starting phenix.real_space_refine (version: dev) on Tue Nov 29 13:10:14 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dls_27514/11_2022/8dls_27514.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dls_27514/11_2022/8dls_27514.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dls_27514/11_2022/8dls_27514.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dls_27514/11_2022/8dls_27514.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dls_27514/11_2022/8dls_27514.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dls_27514/11_2022/8dls_27514.pdb" } resolution = 2.66 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= -0.000 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 132": "OE1" <-> "OE2" Residue "A PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 198": "OD1" <-> "OD2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A ASP 228": "OD1" <-> "OD2" Residue "H TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 91": "OE1" <-> "OE2" Residue "H GLU 108": "OE1" <-> "OE2" Residue "H TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 129": "OD1" <-> "OD2" Residue "H TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 4017 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2081 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 12, 'TRANS': 242} Chain breaks: 3 Chain: "H" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 976 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 4, 'TRANS': 123} Chain: "L" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 862 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 103} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 2.78, per 1000 atoms: 0.69 Number of scatterers: 4017 At special positions: 0 Unit cell: (95, 61, 101, 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 18 16.00 O 785 8.00 N 648 7.00 C 2566 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.03 Simple disulfide: pdb=" SG CYS L 43 " - pdb=" SG CYS L 113 " distance=2.03 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 149 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG B 1 " - " ASN A 122 " Time building additional restraints: 1.54 Conformation dependent library (CDL) restraints added in 684.6 milliseconds 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 920 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 10 sheets defined 2.6% alpha, 45.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'H' and resid 47 through 49 No H-bonds generated for 'chain 'H' and resid 47 through 49' Processing helix chain 'H' and resid 106 through 110 removed outlier: 3.910A pdb=" N THR H 110 " --> pdb=" O SER H 107 " (cutoff:3.500A) Processing helix chain 'L' and resid 104 through 108 removed outlier: 3.963A pdb=" N VAL L 108 " --> pdb=" O ALA L 105 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 30 removed outlier: 8.072A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.764A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.606A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.627A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 11.225A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 9.813A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.170A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.959A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 22 through 25 Processing sheet with id=AA6, first strand: chain 'H' and resid 29 through 31 removed outlier: 6.164A pdb=" N GLU H 29 " --> pdb=" O THR H 144 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR H 141 " --> pdb=" O TYR H 113 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N MET H 53 " --> pdb=" O GLY H 69 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N GLY H 69 " --> pdb=" O MET H 53 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N TRP H 55 " --> pdb=" O MET H 67 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 29 through 31 removed outlier: 6.164A pdb=" N GLU H 29 " --> pdb=" O THR H 144 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR H 141 " --> pdb=" O TYR H 113 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 121 through 123 Processing sheet with id=AA9, first strand: chain 'L' and resid 24 through 27 Processing sheet with id=AB1, first strand: chain 'L' and resid 30 through 32 removed outlier: 3.758A pdb=" N ASP L 130 " --> pdb=" O SER L 31 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N GLN L 62 " --> pdb=" O LEU L 71 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N LEU L 71 " --> pdb=" O GLN L 62 " (cutoff:3.500A) 144 hydrogen bonds defined for protein. 357 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: 1.25 Time building geometry restraints manager: 1.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1235 1.34 - 1.46: 1022 1.46 - 1.58: 1834 1.58 - 1.70: 0 1.70 - 1.81: 27 Bond restraints: 4118 Sorted by residual: bond pdb=" C ARG A 102 " pdb=" N GLY A 103 " ideal model delta sigma weight residual 1.327 1.307 0.020 1.11e-02 8.12e+03 3.25e+00 bond pdb=" CG LEU L 58 " pdb=" CD1 LEU L 58 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.33e+00 bond pdb=" C GLY A 35 " pdb=" N VAL A 36 " ideal model delta sigma weight residual 1.329 1.302 0.027 1.96e-02 2.60e+03 1.91e+00 bond pdb=" C ASP A 228 " pdb=" N LEU A 229 " ideal model delta sigma weight residual 1.332 1.313 0.019 1.44e-02 4.82e+03 1.80e+00 bond pdb=" CA ASP A 198 " pdb=" CB ASP A 198 " ideal model delta sigma weight residual 1.530 1.551 -0.021 1.69e-02 3.50e+03 1.54e+00 ... (remaining 4113 not shown) Histogram of bond angle deviations from ideal: 98.65 - 105.71: 88 105.71 - 112.77: 2131 112.77 - 119.82: 1326 119.82 - 126.88: 1996 126.88 - 133.94: 56 Bond angle restraints: 5597 Sorted by residual: angle pdb=" C ILE A 197 " pdb=" N ASP A 198 " pdb=" CA ASP A 198 " ideal model delta sigma weight residual 121.54 132.21 -10.67 1.91e+00 2.74e-01 3.12e+01 angle pdb=" CA LEU H 127 " pdb=" CB LEU H 127 " pdb=" CG LEU H 127 " ideal model delta sigma weight residual 116.30 128.67 -12.37 3.50e+00 8.16e-02 1.25e+01 angle pdb=" C2 NAG A1305 " pdb=" N2 NAG A1305 " pdb=" C7 NAG A1305 " ideal model delta sigma weight residual 123.12 127.29 -4.17 1.28e+00 6.08e-01 1.06e+01 angle pdb=" C GLN H 139 " pdb=" N GLY H 140 " pdb=" CA GLY H 140 " ideal model delta sigma weight residual 122.73 119.73 3.00 9.30e-01 1.16e+00 1.04e+01 angle pdb=" CA THR L 56 " pdb=" CB THR L 56 " pdb=" CG2 THR L 56 " ideal model delta sigma weight residual 110.50 115.81 -5.31 1.70e+00 3.46e-01 9.77e+00 ... (remaining 5592 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 2232 17.40 - 34.79: 137 34.79 - 52.18: 21 52.18 - 69.57: 4 69.57 - 86.97: 5 Dihedral angle restraints: 2399 sinusoidal: 961 harmonic: 1438 Sorted by residual: dihedral pdb=" CA ASN A 149 " pdb=" C ASN A 149 " pdb=" N LYS A 150 " pdb=" CA LYS A 150 " ideal model delta harmonic sigma weight residual 180.00 150.54 29.46 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA LYS H 31 " pdb=" C LYS H 31 " pdb=" N LYS H 32 " pdb=" CA LYS H 32 " ideal model delta harmonic sigma weight residual 180.00 157.28 22.72 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA ILE A 128 " pdb=" C ILE A 128 " pdb=" N LYS A 129 " pdb=" CA LYS A 129 " ideal model delta harmonic sigma weight residual 180.00 -159.53 -20.47 0 5.00e+00 4.00e-02 1.68e+01 ... (remaining 2396 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 576 0.097 - 0.193: 53 0.193 - 0.290: 3 0.290 - 0.386: 0 0.386 - 0.483: 3 Chirality restraints: 635 Sorted by residual: chirality pdb=" C1 NAG A1303 " pdb=" ND2 ASN A 165 " pdb=" C2 NAG A1303 " pdb=" O5 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.83e+00 chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A 149 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.25e+00 chirality pdb=" CB THR L 56 " pdb=" CA THR L 56 " pdb=" OG1 THR L 56 " pdb=" CG2 THR L 56 " both_signs ideal model delta sigma weight residual False 2.55 2.14 0.41 2.00e-01 2.50e+01 4.19e+00 ... (remaining 632 not shown) Planarity restraints: 711 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 149 " 0.005 2.00e-02 2.50e+03 2.66e-02 8.87e+00 pdb=" CG ASN A 149 " -0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN A 149 " 0.031 2.00e-02 2.50e+03 pdb=" ND2 ASN A 149 " -0.027 2.00e-02 2.50e+03 pdb=" C1 NAG A1302 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 198 " -0.014 2.00e-02 2.50e+03 2.74e-02 7.53e+00 pdb=" CG ASP A 198 " 0.047 2.00e-02 2.50e+03 pdb=" OD1 ASP A 198 " -0.018 2.00e-02 2.50e+03 pdb=" OD2 ASP A 198 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL L 83 " 0.042 5.00e-02 4.00e+02 6.39e-02 6.53e+00 pdb=" N PRO L 84 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO L 84 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO L 84 " 0.035 5.00e-02 4.00e+02 ... (remaining 708 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1088 2.81 - 3.33: 3098 3.33 - 3.86: 6567 3.86 - 4.38: 7546 4.38 - 4.90: 13461 Nonbonded interactions: 31760 Sorted by model distance: nonbonded pdb=" OD1 ASP H 109 " pdb=" OH TYR H 113 " model vdw 2.288 2.440 nonbonded pdb=" OG SER L 90 " pdb=" OG1 THR L 97 " model vdw 2.323 2.440 nonbonded pdb=" OG1 THR H 124 " pdb=" O ASP H 126 " model vdw 2.327 2.440 nonbonded pdb=" OG1 THR A 109 " pdb=" OD1 ASP A 111 " model vdw 2.362 2.440 nonbonded pdb=" O SER H 147 " pdb=" OG SER H 147 " model vdw 2.374 2.440 ... (remaining 31755 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 18 5.16 5 C 2566 2.51 5 N 648 2.21 5 O 785 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 2.380 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: 12.740 Check model and map are aligned: 0.060 Convert atoms to be neutral: 0.040 Process input model: 16.370 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.050 4118 Z= 0.376 Angle : 0.895 12.370 5597 Z= 0.486 Chirality : 0.062 0.483 635 Planarity : 0.007 0.069 705 Dihedral : 12.273 86.966 1467 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.59 (0.37), residues: 483 helix: None (None), residues: 0 sheet: 0.15 (0.36), residues: 218 loop : -0.84 (0.36), residues: 265 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.442 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 1.0065 time to fit residues: 102.5606 Evaluate side-chains 81 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.456 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 28 optimal weight: 6.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 207 HIS L 78 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 4118 Z= 0.249 Angle : 0.601 10.664 5597 Z= 0.310 Chirality : 0.050 0.416 635 Planarity : 0.004 0.048 705 Dihedral : 5.375 25.360 579 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer Outliers : 2.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.17 (0.38), residues: 483 helix: None (None), residues: 0 sheet: 0.30 (0.35), residues: 218 loop : -0.41 (0.38), residues: 265 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 85 time to evaluate : 0.445 Fit side-chains outliers start: 9 outliers final: 9 residues processed: 87 average time/residue: 0.9044 time to fit residues: 82.2693 Evaluate side-chains 87 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 78 time to evaluate : 0.492 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 2 residues processed: 7 average time/residue: 0.2189 time to fit residues: 2.4007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 29 optimal weight: 0.0470 chunk 12 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 38 optimal weight: 0.1980 chunk 14 optimal weight: 1.9990 chunk 35 optimal weight: 0.0370 chunk 32 optimal weight: 3.9990 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 4118 Z= 0.242 Angle : 0.582 10.091 5597 Z= 0.297 Chirality : 0.048 0.369 635 Planarity : 0.004 0.042 705 Dihedral : 5.130 21.888 579 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer Outliers : 2.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.03 (0.39), residues: 483 helix: None (None), residues: 0 sheet: 0.33 (0.36), residues: 217 loop : -0.24 (0.39), residues: 266 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 83 time to evaluate : 0.480 Fit side-chains outliers start: 12 outliers final: 9 residues processed: 85 average time/residue: 0.8974 time to fit residues: 79.7930 Evaluate side-chains 87 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 78 time to evaluate : 0.498 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 2 residues processed: 7 average time/residue: 0.0615 time to fit residues: 1.3092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 22 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 29 optimal weight: 0.0470 chunk 43 optimal weight: 0.0570 chunk 46 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 38 optimal weight: 0.2980 chunk 26 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 4118 Z= 0.190 Angle : 0.559 10.908 5597 Z= 0.283 Chirality : 0.046 0.324 635 Planarity : 0.004 0.040 705 Dihedral : 4.905 19.429 579 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer Outliers : 3.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.18 (0.40), residues: 483 helix: None (None), residues: 0 sheet: 0.46 (0.36), residues: 221 loop : -0.09 (0.40), residues: 262 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 84 time to evaluate : 0.493 Fit side-chains outliers start: 14 outliers final: 10 residues processed: 89 average time/residue: 0.8788 time to fit residues: 81.8257 Evaluate side-chains 87 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 77 time to evaluate : 0.472 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 2 residues processed: 8 average time/residue: 0.1610 time to fit residues: 2.1724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 34 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 41 optimal weight: 0.0060 chunk 11 optimal weight: 1.9990 chunk 15 optimal weight: 0.4980 chunk 9 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 4118 Z= 0.248 Angle : 0.588 11.436 5597 Z= 0.296 Chirality : 0.047 0.306 635 Planarity : 0.004 0.040 705 Dihedral : 4.908 17.558 579 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer Outliers : 2.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.24 (0.40), residues: 483 helix: None (None), residues: 0 sheet: 0.53 (0.37), residues: 206 loop : -0.04 (0.39), residues: 277 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 78 time to evaluate : 0.507 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 10 residues processed: 83 average time/residue: 1.0438 time to fit residues: 90.2447 Evaluate side-chains 85 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 75 time to evaluate : 0.439 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 3 residues processed: 7 average time/residue: 0.0620 time to fit residues: 1.2851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 11 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 38 optimal weight: 0.3980 chunk 21 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 15 optimal weight: 0.0870 chunk 24 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 4118 Z= 0.222 Angle : 0.573 11.963 5597 Z= 0.288 Chirality : 0.046 0.283 635 Planarity : 0.004 0.040 705 Dihedral : 4.787 16.536 579 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer Outliers : 1.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.24 (0.39), residues: 483 helix: None (None), residues: 0 sheet: 0.49 (0.38), residues: 200 loop : -0.01 (0.38), residues: 283 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 79 time to evaluate : 0.547 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 83 average time/residue: 1.0417 time to fit residues: 90.2413 Evaluate side-chains 79 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 75 time to evaluate : 0.470 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.0406 time to fit residues: 0.7003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 26 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 21 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 27 optimal weight: 0.0770 chunk 13 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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: 0.8263 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 4118 Z= 0.218 Angle : 0.583 12.464 5597 Z= 0.292 Chirality : 0.046 0.276 635 Planarity : 0.004 0.039 705 Dihedral : 4.773 16.167 579 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer Outliers : 2.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.30 (0.39), residues: 483 helix: None (None), residues: 0 sheet: 0.54 (0.37), residues: 206 loop : 0.02 (0.39), residues: 277 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 76 time to evaluate : 0.612 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 11 residues processed: 82 average time/residue: 0.9249 time to fit residues: 79.3475 Evaluate side-chains 86 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 75 time to evaluate : 0.492 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 4 residues processed: 8 average time/residue: 0.1927 time to fit residues: 2.4842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 0.3980 chunk 31 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 4 optimal weight: 0.1980 chunk 36 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 4118 Z= 0.223 Angle : 0.581 13.171 5597 Z= 0.294 Chirality : 0.046 0.277 635 Planarity : 0.004 0.039 705 Dihedral : 4.714 16.179 579 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer Outliers : 2.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.35 (0.39), residues: 483 helix: None (None), residues: 0 sheet: 0.53 (0.38), residues: 193 loop : 0.11 (0.38), residues: 290 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 76 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 83 average time/residue: 1.0161 time to fit residues: 88.0442 Evaluate side-chains 79 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 75 time to evaluate : 0.492 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.0399 time to fit residues: 0.7104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 33 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 28 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 21 optimal weight: 0.3980 chunk 31 optimal weight: 0.4980 chunk 47 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 4118 Z= 0.239 Angle : 0.614 13.761 5597 Z= 0.304 Chirality : 0.046 0.279 635 Planarity : 0.004 0.039 705 Dihedral : 4.791 22.584 579 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer Outliers : 1.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.36 (0.40), residues: 483 helix: None (None), residues: 0 sheet: 0.57 (0.38), residues: 199 loop : 0.09 (0.39), residues: 284 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 77 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 81 average time/residue: 0.9309 time to fit residues: 78.7258 Evaluate side-chains 79 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 75 time to evaluate : 0.486 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 0.6471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 44 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 29 optimal weight: 0.4980 chunk 23 optimal weight: 0.0970 chunk 30 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 35 optimal weight: 0.0970 chunk 5 optimal weight: 0.9980 chunk 10 optimal weight: 0.4980 overall best weight: 0.3776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 4118 Z= 0.189 Angle : 0.607 14.044 5597 Z= 0.301 Chirality : 0.045 0.273 635 Planarity : 0.004 0.042 705 Dihedral : 4.855 21.850 579 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer Outliers : 1.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.28 (0.39), residues: 483 helix: None (None), residues: 0 sheet: 0.54 (0.37), residues: 211 loop : -0.02 (0.39), residues: 272 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 78 time to evaluate : 0.528 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 82 average time/residue: 0.9026 time to fit residues: 77.4098 Evaluate side-chains 78 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 74 time to evaluate : 0.474 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 1 average time/residue: 1.1743 time to fit residues: 1.8439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 38 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 43 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 55 ASN L 118 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.120768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.078126 restraints weight = 6420.771| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 2.83 r_work: 0.3023 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work: 0.3001 rms_B_bonded: 2.60 restraints_weight: 0.1250 r_work: 0.2991 rms_B_bonded: 2.63 restraints_weight: 0.0625 r_work: 0.2980 rms_B_bonded: 2.68 restraints_weight: 0.0312 r_work: 0.2968 rms_B_bonded: 2.75 restraints_weight: 0.0156 r_work: 0.2957 rms_B_bonded: 2.85 restraints_weight: 0.0078 r_work: 0.2945 rms_B_bonded: 2.95 restraints_weight: 0.0039 r_work: 0.2932 rms_B_bonded: 3.08 restraints_weight: 0.0020 r_work: 0.2919 rms_B_bonded: 3.23 restraints_weight: 0.0010 r_work: 0.2906 rms_B_bonded: 3.40 restraints_weight: 0.0005 r_work: 0.2892 rms_B_bonded: 3.59 restraints_weight: 0.0002 r_work: 0.2878 rms_B_bonded: 3.81 restraints_weight: 0.0001 r_work: 0.2863 rms_B_bonded: 4.05 restraints_weight: 0.0001 r_work: 0.2847 rms_B_bonded: 4.32 restraints_weight: 0.0000 r_work: 0.2831 rms_B_bonded: 4.63 restraints_weight: 0.0000 r_work: 0.2814 rms_B_bonded: 4.96 restraints_weight: 0.0000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 4118 Z= 0.266 Angle : 0.628 14.188 5597 Z= 0.313 Chirality : 0.047 0.285 635 Planarity : 0.004 0.045 705 Dihedral : 4.939 20.092 579 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer Outliers : 2.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.27 (0.39), residues: 483 helix: None (None), residues: 0 sheet: 0.49 (0.38), residues: 193 loop : 0.04 (0.38), residues: 290 =============================================================================== Job complete usr+sys time: 2087.95 seconds wall clock time: 38 minutes 1.72 seconds (2281.72 seconds total)