Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 21:11:54 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ot9_13057/04_2023/7ot9_13057.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ot9_13057/04_2023/7ot9_13057.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ot9_13057/04_2023/7ot9_13057.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ot9_13057/04_2023/7ot9_13057.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ot9_13057/04_2023/7ot9_13057.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ot9_13057/04_2023/7ot9_13057.pdb" } resolution = 2.8 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= 0.003 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 55 5.16 5 C 5650 2.51 5 N 1395 2.21 5 O 1310 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 54": "NH1" <-> "NH2" Residue "A ARG 62": "NH1" <-> "NH2" Residue "A ARG 180": "NH1" <-> "NH2" Residue "A GLU 182": "OE1" <-> "OE2" Residue "A ARG 301": "NH1" <-> "NH2" Residue "A GLU 347": "OE1" <-> "OE2" Residue "E ARG 54": "NH1" <-> "NH2" Residue "E ARG 62": "NH1" <-> "NH2" Residue "E ARG 180": "NH1" <-> "NH2" Residue "E GLU 182": "OE1" <-> "OE2" Residue "E ARG 301": "NH1" <-> "NH2" Residue "E GLU 347": "OE1" <-> "OE2" Residue "D ARG 54": "NH1" <-> "NH2" Residue "D ARG 62": "NH1" <-> "NH2" Residue "D ARG 180": "NH1" <-> "NH2" Residue "D GLU 182": "OE1" <-> "OE2" Residue "D ARG 301": "NH1" <-> "NH2" Residue "D GLU 347": "OE1" <-> "OE2" Residue "C ARG 54": "NH1" <-> "NH2" Residue "C ARG 62": "NH1" <-> "NH2" Residue "C ARG 180": "NH1" <-> "NH2" Residue "C GLU 182": "OE1" <-> "OE2" Residue "C ARG 301": "NH1" <-> "NH2" Residue "C GLU 347": "OE1" <-> "OE2" Residue "B ARG 54": "NH1" <-> "NH2" Residue "B ARG 62": "NH1" <-> "NH2" Residue "B ARG 180": "NH1" <-> "NH2" Residue "B GLU 182": "OE1" <-> "OE2" Residue "B ARG 301": "NH1" <-> "NH2" Residue "B GLU 347": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 8410 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1682 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 8, 'TRANS': 212} Chain breaks: 2 Chain: "E" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1682 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 8, 'TRANS': 212} Chain breaks: 2 Chain: "D" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1682 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 8, 'TRANS': 212} Chain breaks: 2 Chain: "C" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1682 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 8, 'TRANS': 212} Chain breaks: 2 Chain: "B" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1682 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 8, 'TRANS': 212} Chain breaks: 2 Time building chain proxies: 4.96, per 1000 atoms: 0.59 Number of scatterers: 8410 At special positions: 0 Unit cell: (126.312, 125.204, 60.94, 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 55 16.00 O 1310 8.00 N 1395 7.00 C 5650 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: 3.82 Conformation dependent library (CDL) restraints added in 1.2 seconds 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2010 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 0 sheets defined 86.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 9 through 48 Proline residue: A 33 - end of helix removed outlier: 4.468A pdb=" N LEU A 36 " --> pdb=" O GLN A 32 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N GLY A 37 " --> pdb=" O PRO A 33 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY A 42 " --> pdb=" O PHE A 38 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N VAL A 45 " --> pdb=" O ALA A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 59 Processing helix chain 'A' and resid 62 through 79 Processing helix chain 'A' and resid 167 through 180 Processing helix chain 'A' and resid 180 through 196 Processing helix chain 'A' and resid 198 through 230 removed outlier: 3.997A pdb=" N GLY A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 289 removed outlier: 3.749A pdb=" N LEU A 281 " --> pdb=" O TRP A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 306 Processing helix chain 'A' and resid 307 through 322 Processing helix chain 'A' and resid 325 through 346 Proline residue: A 331 - end of helix Processing helix chain 'E' and resid 9 through 48 Proline residue: E 33 - end of helix removed outlier: 4.468A pdb=" N LEU E 36 " --> pdb=" O GLN E 32 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N GLY E 37 " --> pdb=" O PRO E 33 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY E 42 " --> pdb=" O PHE E 38 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N VAL E 45 " --> pdb=" O ALA E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 59 Processing helix chain 'E' and resid 62 through 79 Processing helix chain 'E' and resid 167 through 180 Processing helix chain 'E' and resid 180 through 196 Processing helix chain 'E' and resid 198 through 230 removed outlier: 3.996A pdb=" N GLY E 230 " --> pdb=" O ALA E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 289 removed outlier: 3.749A pdb=" N LEU E 281 " --> pdb=" O TRP E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 306 Processing helix chain 'E' and resid 307 through 322 Processing helix chain 'E' and resid 325 through 346 Proline residue: E 331 - end of helix Processing helix chain 'D' and resid 9 through 48 Proline residue: D 33 - end of helix removed outlier: 4.468A pdb=" N LEU D 36 " --> pdb=" O GLN D 32 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N GLY D 37 " --> pdb=" O PRO D 33 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY D 42 " --> pdb=" O PHE D 38 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N VAL D 45 " --> pdb=" O ALA D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 59 Processing helix chain 'D' and resid 62 through 79 Processing helix chain 'D' and resid 167 through 180 Processing helix chain 'D' and resid 180 through 196 Processing helix chain 'D' and resid 198 through 230 removed outlier: 3.997A pdb=" N GLY D 230 " --> pdb=" O ALA D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 289 removed outlier: 3.748A pdb=" N LEU D 281 " --> pdb=" O TRP D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 306 Processing helix chain 'D' and resid 307 through 322 Processing helix chain 'D' and resid 325 through 346 Proline residue: D 331 - end of helix Processing helix chain 'C' and resid 9 through 48 Proline residue: C 33 - end of helix removed outlier: 4.468A pdb=" N LEU C 36 " --> pdb=" O GLN C 32 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N GLY C 37 " --> pdb=" O PRO C 33 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY C 42 " --> pdb=" O PHE C 38 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N VAL C 45 " --> pdb=" O ALA C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 59 Processing helix chain 'C' and resid 62 through 79 Processing helix chain 'C' and resid 167 through 180 Processing helix chain 'C' and resid 180 through 196 Processing helix chain 'C' and resid 198 through 230 removed outlier: 3.997A pdb=" N GLY C 230 " --> pdb=" O ALA C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 289 removed outlier: 3.749A pdb=" N LEU C 281 " --> pdb=" O TRP C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 306 Processing helix chain 'C' and resid 307 through 322 Processing helix chain 'C' and resid 325 through 346 Proline residue: C 331 - end of helix Processing helix chain 'B' and resid 9 through 48 Proline residue: B 33 - end of helix removed outlier: 4.468A pdb=" N LEU B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N GLY B 37 " --> pdb=" O PRO B 33 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY B 42 " --> pdb=" O PHE B 38 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N VAL B 45 " --> pdb=" O ALA B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 59 Processing helix chain 'B' and resid 62 through 79 Processing helix chain 'B' and resid 167 through 180 Processing helix chain 'B' and resid 180 through 196 Processing helix chain 'B' and resid 198 through 230 removed outlier: 3.997A pdb=" N GLY B 230 " --> pdb=" O ALA B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 289 removed outlier: 3.749A pdb=" N LEU B 281 " --> pdb=" O TRP B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 306 Processing helix chain 'B' and resid 307 through 322 Processing helix chain 'B' and resid 325 through 346 Proline residue: B 331 - end of helix 695 hydrogen bonds defined for protein. 2055 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: 2.28 Time building geometry restraints manager: 4.08 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: 2565 1.34 - 1.46: 1319 1.46 - 1.57: 4606 1.57 - 1.69: 0 1.69 - 1.81: 100 Bond restraints: 8590 Sorted by residual: bond pdb=" C ALA C 41 " pdb=" N GLY C 42 " ideal model delta sigma weight residual 1.331 1.316 0.015 1.46e-02 4.69e+03 1.01e+00 bond pdb=" C ALA D 41 " pdb=" N GLY D 42 " ideal model delta sigma weight residual 1.331 1.316 0.014 1.46e-02 4.69e+03 9.84e-01 bond pdb=" C ALA A 41 " pdb=" N GLY A 42 " ideal model delta sigma weight residual 1.331 1.316 0.014 1.46e-02 4.69e+03 9.59e-01 bond pdb=" C ALA B 41 " pdb=" N GLY B 42 " ideal model delta sigma weight residual 1.331 1.317 0.014 1.46e-02 4.69e+03 9.11e-01 bond pdb=" C ALA E 41 " pdb=" N GLY E 42 " ideal model delta sigma weight residual 1.331 1.317 0.014 1.46e-02 4.69e+03 9.03e-01 ... (remaining 8585 not shown) Histogram of bond angle deviations from ideal: 99.26 - 106.21: 237 106.21 - 113.15: 5038 113.15 - 120.09: 2809 120.09 - 127.03: 3492 127.03 - 133.98: 154 Bond angle restraints: 11730 Sorted by residual: angle pdb=" N VAL E 198 " pdb=" CA VAL E 198 " pdb=" C VAL E 198 " ideal model delta sigma weight residual 113.53 108.12 5.41 9.80e-01 1.04e+00 3.05e+01 angle pdb=" N VAL B 198 " pdb=" CA VAL B 198 " pdb=" C VAL B 198 " ideal model delta sigma weight residual 113.53 108.15 5.38 9.80e-01 1.04e+00 3.01e+01 angle pdb=" N VAL C 198 " pdb=" CA VAL C 198 " pdb=" C VAL C 198 " ideal model delta sigma weight residual 113.53 108.16 5.37 9.80e-01 1.04e+00 3.01e+01 angle pdb=" N VAL A 198 " pdb=" CA VAL A 198 " pdb=" C VAL A 198 " ideal model delta sigma weight residual 113.53 108.16 5.37 9.80e-01 1.04e+00 3.00e+01 angle pdb=" N VAL D 198 " pdb=" CA VAL D 198 " pdb=" C VAL D 198 " ideal model delta sigma weight residual 113.53 108.16 5.37 9.80e-01 1.04e+00 3.00e+01 ... (remaining 11725 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 4470 17.70 - 35.40: 410 35.40 - 53.10: 45 53.10 - 70.80: 10 70.80 - 88.49: 15 Dihedral angle restraints: 4950 sinusoidal: 1845 harmonic: 3105 Sorted by residual: dihedral pdb=" CA ASN A 293 " pdb=" C ASN A 293 " pdb=" N VAL A 294 " pdb=" CA VAL A 294 " ideal model delta harmonic sigma weight residual -180.00 -160.95 -19.05 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA ASN C 293 " pdb=" C ASN C 293 " pdb=" N VAL C 294 " pdb=" CA VAL C 294 " ideal model delta harmonic sigma weight residual -180.00 -160.98 -19.02 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA ASN D 293 " pdb=" C ASN D 293 " pdb=" N VAL D 294 " pdb=" CA VAL D 294 " ideal model delta harmonic sigma weight residual 180.00 -160.99 -19.01 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 4947 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 840 0.031 - 0.062: 479 0.062 - 0.092: 124 0.092 - 0.123: 37 0.123 - 0.154: 10 Chirality restraints: 1490 Sorted by residual: chirality pdb=" CB ILE E 300 " pdb=" CA ILE E 300 " pdb=" CG1 ILE E 300 " pdb=" CG2 ILE E 300 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.15 2.00e-01 2.50e+01 5.92e-01 chirality pdb=" CB ILE A 300 " pdb=" CA ILE A 300 " pdb=" CG1 ILE A 300 " pdb=" CG2 ILE A 300 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.15 2.00e-01 2.50e+01 5.85e-01 chirality pdb=" CB ILE B 300 " pdb=" CA ILE B 300 " pdb=" CG1 ILE B 300 " pdb=" CG2 ILE B 300 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.15 2.00e-01 2.50e+01 5.84e-01 ... (remaining 1487 not shown) Planarity restraints: 1385 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY C 42 " -0.012 2.00e-02 2.50e+03 2.34e-02 5.46e+00 pdb=" C GLY C 42 " 0.040 2.00e-02 2.50e+03 pdb=" O GLY C 42 " -0.015 2.00e-02 2.50e+03 pdb=" N THR C 43 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 42 " 0.012 2.00e-02 2.50e+03 2.32e-02 5.39e+00 pdb=" C GLY B 42 " -0.040 2.00e-02 2.50e+03 pdb=" O GLY B 42 " 0.015 2.00e-02 2.50e+03 pdb=" N THR B 43 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 42 " -0.012 2.00e-02 2.50e+03 2.31e-02 5.32e+00 pdb=" C GLY D 42 " 0.040 2.00e-02 2.50e+03 pdb=" O GLY D 42 " -0.015 2.00e-02 2.50e+03 pdb=" N THR D 43 " -0.014 2.00e-02 2.50e+03 ... (remaining 1382 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 103 2.69 - 3.24: 8869 3.24 - 3.80: 13722 3.80 - 4.35: 15471 4.35 - 4.90: 27598 Nonbonded interactions: 65763 Sorted by model distance: nonbonded pdb=" O TRP D 344 " pdb=" NH1 ARG C 194 " model vdw 2.138 2.520 nonbonded pdb=" OG1 THR C 48 " pdb=" OH TYR C 178 " model vdw 2.140 2.440 nonbonded pdb=" OG1 THR E 48 " pdb=" OH TYR E 178 " model vdw 2.140 2.440 nonbonded pdb=" OG1 THR D 48 " pdb=" OH TYR D 178 " model vdw 2.141 2.440 nonbonded pdb=" OG1 THR A 48 " pdb=" OH TYR A 178 " model vdw 2.141 2.440 ... (remaining 65758 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' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.590 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: 3.610 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 24.990 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.040 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:14.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 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 : 0.005 0.030 8590 Z= 0.319 Angle : 0.667 6.000 11730 Z= 0.365 Chirality : 0.040 0.154 1490 Planarity : 0.004 0.023 1385 Dihedral : 14.505 88.495 2940 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.25), residues: 1075 helix: 2.27 (0.17), residues: 905 sheet: None (None), residues: 0 loop : -2.04 (0.44), residues: 170 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 0.969 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 1.2074 time to fit residues: 146.8115 Evaluate side-chains 84 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.971 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.5980 chunk 83 optimal weight: 0.0070 chunk 46 optimal weight: 0.0030 chunk 28 optimal weight: 0.8980 chunk 56 optimal weight: 7.9990 chunk 44 optimal weight: 0.6980 chunk 86 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 chunk 99 optimal weight: 0.8980 overall best weight: 0.4008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.0998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 8590 Z= 0.164 Angle : 0.610 7.130 11730 Z= 0.299 Chirality : 0.037 0.122 1490 Planarity : 0.005 0.052 1385 Dihedral : 4.392 20.683 1155 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer Outliers : 1.14 % 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: 2.99 (0.25), residues: 1075 helix: 2.82 (0.17), residues: 870 sheet: None (None), residues: 0 loop : -2.02 (0.40), residues: 205 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 99 time to evaluate : 1.032 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 104 average time/residue: 1.2377 time to fit residues: 137.2435 Evaluate side-chains 96 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 88 time to evaluate : 0.984 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 5 residues processed: 3 average time/residue: 0.0752 time to fit residues: 1.7258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.027 8590 Z= 0.271 Angle : 0.590 7.345 11730 Z= 0.289 Chirality : 0.037 0.111 1490 Planarity : 0.004 0.030 1385 Dihedral : 4.284 20.815 1155 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer Outliers : 2.40 % 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: 2.94 (0.25), residues: 1075 helix: 2.79 (0.17), residues: 875 sheet: None (None), residues: 0 loop : -2.19 (0.39), residues: 200 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 93 time to evaluate : 1.152 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 9 residues processed: 103 average time/residue: 1.1721 time to fit residues: 129.1054 Evaluate side-chains 96 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 87 time to evaluate : 0.954 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 5 residues processed: 4 average time/residue: 0.1170 time to fit residues: 2.1455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 51 optimal weight: 10.0000 chunk 11 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 GLN ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 8590 Z= 0.180 Angle : 0.561 7.836 11730 Z= 0.274 Chirality : 0.036 0.112 1490 Planarity : 0.004 0.030 1385 Dihedral : 4.220 20.604 1155 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer Outliers : 2.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.13 (0.26), residues: 1075 helix: 2.90 (0.17), residues: 875 sheet: None (None), residues: 0 loop : -2.04 (0.39), residues: 200 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 95 time to evaluate : 0.933 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 14 residues processed: 110 average time/residue: 1.0194 time to fit residues: 120.8859 Evaluate side-chains 103 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 89 time to evaluate : 0.946 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 10 residues processed: 4 average time/residue: 0.0805 time to fit residues: 1.9267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.9990 chunk 60 optimal weight: 40.0000 chunk 1 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 43 optimal weight: 0.0000 chunk 90 optimal weight: 0.6980 chunk 73 optimal weight: 0.1980 chunk 0 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 95 optimal weight: 7.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 8590 Z= 0.148 Angle : 0.530 8.105 11730 Z= 0.261 Chirality : 0.036 0.126 1490 Planarity : 0.004 0.032 1385 Dihedral : 4.130 20.058 1155 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer Outliers : 2.17 % 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: 3.27 (0.26), residues: 1075 helix: 2.99 (0.17), residues: 875 sheet: None (None), residues: 0 loop : -1.95 (0.40), residues: 200 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 92 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 14 residues processed: 107 average time/residue: 1.1099 time to fit residues: 127.5563 Evaluate side-chains 103 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 89 time to evaluate : 1.044 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 11 residues processed: 3 average time/residue: 0.0721 time to fit residues: 1.6727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 88 optimal weight: 0.4980 chunk 49 optimal weight: 0.4980 chunk 8 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 102 optimal weight: 7.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 8590 Z= 0.176 Angle : 0.530 8.873 11730 Z= 0.260 Chirality : 0.036 0.110 1490 Planarity : 0.004 0.033 1385 Dihedral : 4.102 20.061 1155 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer Outliers : 1.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.31 (0.26), residues: 1075 helix: 3.02 (0.17), residues: 875 sheet: None (None), residues: 0 loop : -1.98 (0.40), residues: 200 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 91 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 14 residues processed: 107 average time/residue: 1.0695 time to fit residues: 122.8350 Evaluate side-chains 103 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 89 time to evaluate : 0.971 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 13 residues processed: 1 average time/residue: 1.0321 time to fit residues: 2.3380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 77 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 106 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 8590 Z= 0.158 Angle : 0.536 10.901 11730 Z= 0.262 Chirality : 0.036 0.130 1490 Planarity : 0.004 0.032 1385 Dihedral : 4.045 19.654 1155 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer Outliers : 2.63 % 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: 3.41 (0.26), residues: 1075 helix: 3.09 (0.17), residues: 875 sheet: None (None), residues: 0 loop : -1.92 (0.40), residues: 200 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 94 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 16 residues processed: 114 average time/residue: 1.0260 time to fit residues: 127.0510 Evaluate side-chains 108 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 92 time to evaluate : 0.974 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 13 residues processed: 3 average time/residue: 0.0856 time to fit residues: 1.7705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.3980 chunk 31 optimal weight: 0.7980 chunk 20 optimal weight: 6.9990 chunk 67 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 101 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 8590 Z= 0.160 Angle : 0.553 11.550 11730 Z= 0.268 Chirality : 0.036 0.116 1490 Planarity : 0.004 0.032 1385 Dihedral : 4.021 19.546 1155 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer Outliers : 2.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.46 (0.26), residues: 1075 helix: 3.12 (0.17), residues: 875 sheet: None (None), residues: 0 loop : -1.89 (0.40), residues: 200 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 96 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 13 residues processed: 119 average time/residue: 0.9949 time to fit residues: 127.7821 Evaluate side-chains 104 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 91 time to evaluate : 0.951 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 13 residues processed: 0 time to fit residues: 1.3610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 89 optimal weight: 0.9980 chunk 93 optimal weight: 0.4980 chunk 64 optimal weight: 0.6980 chunk 104 optimal weight: 20.0000 chunk 63 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 8590 Z= 0.170 Angle : 0.580 12.463 11730 Z= 0.280 Chirality : 0.036 0.150 1490 Planarity : 0.004 0.032 1385 Dihedral : 4.001 19.509 1155 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer Outliers : 2.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.52 (0.26), residues: 1075 helix: 3.17 (0.17), residues: 875 sheet: None (None), residues: 0 loop : -1.91 (0.41), residues: 200 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 93 time to evaluate : 1.031 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 15 residues processed: 117 average time/residue: 1.0223 time to fit residues: 128.8412 Evaluate side-chains 107 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 92 time to evaluate : 0.907 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 15 residues processed: 0 time to fit residues: 1.2227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 chunk 87 optimal weight: 0.0470 chunk 9 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 92 optimal weight: 8.9990 chunk 26 optimal weight: 0.1980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 8590 Z= 0.159 Angle : 0.607 13.465 11730 Z= 0.291 Chirality : 0.036 0.157 1490 Planarity : 0.004 0.033 1385 Dihedral : 3.997 19.313 1155 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer Outliers : 1.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.54 (0.26), residues: 1075 helix: 3.18 (0.17), residues: 875 sheet: None (None), residues: 0 loop : -1.86 (0.42), residues: 200 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 96 time to evaluate : 1.142 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 15 residues processed: 113 average time/residue: 1.1123 time to fit residues: 134.9306 Evaluate side-chains 103 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 88 time to evaluate : 1.039 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 15 residues processed: 0 time to fit residues: 1.3630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 89 optimal weight: 0.6980 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 30.0000 chunk 76 optimal weight: 4.9990 chunk 4 optimal weight: 0.0980 chunk 63 optimal weight: 0.0670 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 GLN ** 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 = 0.3736 r_free = 0.3736 target = 0.103429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.074177 restraints weight = 18276.487| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.84 r_work: 0.3042 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 8590 Z= 0.157 Angle : 0.602 13.387 11730 Z= 0.288 Chirality : 0.035 0.118 1490 Planarity : 0.004 0.033 1385 Dihedral : 3.938 19.193 1155 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer Outliers : 2.40 % 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: 3.54 (0.26), residues: 1075 helix: 3.17 (0.17), residues: 875 sheet: None (None), residues: 0 loop : -1.82 (0.42), residues: 200 =============================================================================== Job complete usr+sys time: 2661.05 seconds wall clock time: 47 minutes 52.86 seconds (2872.86 seconds total)