Starting phenix.real_space_refine (version: 1.21rc1) on Tue Oct 3 02:46:37 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cxr_30495/10_2023/7cxr_30495.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cxr_30495/10_2023/7cxr_30495.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cxr_30495/10_2023/7cxr_30495.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cxr_30495/10_2023/7cxr_30495.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cxr_30495/10_2023/7cxr_30495.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cxr_30495/10_2023/7cxr_30495.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.084 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 28 5.16 5 C 3406 2.51 5 N 858 2.21 5 O 876 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 14": "NH1" <-> "NH2" Residue "A ARG 31": "NH1" <-> "NH2" Residue "A GLU 38": "OE1" <-> "OE2" Residue "A GLU 39": "OE1" <-> "OE2" Residue "A ARG 57": "NH1" <-> "NH2" Residue "A GLU 75": "OE1" <-> "OE2" Residue "A GLU 89": "OE1" <-> "OE2" Residue "A GLU 132": "OE1" <-> "OE2" Residue "A ARG 152": "NH1" <-> "NH2" Residue "B ARG 14": "NH1" <-> "NH2" Residue "B ARG 31": "NH1" <-> "NH2" Residue "B GLU 38": "OE1" <-> "OE2" Residue "B GLU 39": "OE1" <-> "OE2" Residue "B ARG 57": "NH1" <-> "NH2" Residue "B GLU 75": "OE1" <-> "OE2" Residue "B GLU 89": "OE1" <-> "OE2" Residue "B GLU 132": "OE1" <-> "OE2" Residue "B ARG 152": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 5168 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2584 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 7, 'TRANS': 299} Chain breaks: 1 Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2584 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 7, 'TRANS': 299} Chain breaks: 1 Time building chain proxies: 3.39, per 1000 atoms: 0.66 Number of scatterers: 5168 At special positions: 0 Unit cell: (90.221, 114.135, 93.482, 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 28 16.00 O 876 8.00 N 858 7.00 C 3406 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.87 Conformation dependent library (CDL) restraints added in 721.1 milliseconds 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1172 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 0 sheets defined 88.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 9 through 69 removed outlier: 3.811A pdb=" N GLN A 21 " --> pdb=" O GLU A 17 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N SER A 49 " --> pdb=" O ASN A 45 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER A 50 " --> pdb=" O ASN A 46 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU A 58 " --> pdb=" O GLN A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 99 removed outlier: 3.594A pdb=" N LYS A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N GLU A 89 " --> pdb=" O ASN A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 114 Processing helix chain 'A' and resid 122 through 154 Processing helix chain 'A' and resid 157 through 186 Processing helix chain 'A' and resid 191 through 208 removed outlier: 4.360A pdb=" N PHE A 195 " --> pdb=" O GLY A 191 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N HIS A 197 " --> pdb=" O TRP A 193 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE A 202 " --> pdb=" O TYR A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 236 removed outlier: 5.740A pdb=" N ASN A 221 " --> pdb=" O GLN A 217 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N GLN A 222 " --> pdb=" O LYS A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 243 removed outlier: 4.386A pdb=" N TYR A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 297 removed outlier: 4.138A pdb=" N THR A 273 " --> pdb=" O TRP A 269 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N PHE A 274 " --> pdb=" O ARG A 270 " (cutoff:3.500A) Proline residue: A 277 - end of helix Processing helix chain 'A' and resid 305 through 338 Proline residue: A 313 - end of helix Processing helix chain 'B' and resid 9 through 69 removed outlier: 3.811A pdb=" N GLN B 21 " --> pdb=" O GLU B 17 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER B 49 " --> pdb=" O ASN B 45 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER B 50 " --> pdb=" O ASN B 46 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU B 58 " --> pdb=" O GLN B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 99 removed outlier: 3.594A pdb=" N LYS B 88 " --> pdb=" O GLU B 84 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N GLU B 89 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 114 Processing helix chain 'B' and resid 122 through 154 Processing helix chain 'B' and resid 157 through 186 Processing helix chain 'B' and resid 191 through 208 removed outlier: 4.360A pdb=" N PHE B 195 " --> pdb=" O GLY B 191 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N HIS B 197 " --> pdb=" O TRP B 193 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N PHE B 202 " --> pdb=" O TYR B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 236 removed outlier: 5.740A pdb=" N ASN B 221 " --> pdb=" O GLN B 217 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N GLN B 222 " --> pdb=" O LYS B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 243 removed outlier: 4.386A pdb=" N TYR B 240 " --> pdb=" O LEU B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 297 removed outlier: 4.137A pdb=" N THR B 273 " --> pdb=" O TRP B 269 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N PHE B 274 " --> pdb=" O ARG B 270 " (cutoff:3.500A) Proline residue: B 277 - end of helix Processing helix chain 'B' and resid 305 through 338 Proline residue: B 313 - end of helix 422 hydrogen bonds defined for protein. 1266 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: 1.47 Time building geometry restraints manager: 2.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 788 1.32 - 1.44: 1614 1.44 - 1.57: 2870 1.57 - 1.69: 0 1.69 - 1.81: 42 Bond restraints: 5314 Sorted by residual: bond pdb=" C ILE A 181 " pdb=" O ILE A 181 " ideal model delta sigma weight residual 1.237 1.194 0.043 1.17e-02 7.31e+03 1.34e+01 bond pdb=" C ILE B 181 " pdb=" O ILE B 181 " ideal model delta sigma weight residual 1.237 1.196 0.041 1.17e-02 7.31e+03 1.23e+01 bond pdb=" N ILE A 181 " pdb=" CA ILE A 181 " ideal model delta sigma weight residual 1.461 1.499 -0.039 1.19e-02 7.06e+03 1.06e+01 bond pdb=" N ILE B 181 " pdb=" CA ILE B 181 " ideal model delta sigma weight residual 1.461 1.499 -0.038 1.19e-02 7.06e+03 1.03e+01 bond pdb=" C PRO B 313 " pdb=" O PRO B 313 " ideal model delta sigma weight residual 1.235 1.195 0.040 1.30e-02 5.92e+03 9.36e+00 ... (remaining 5309 not shown) Histogram of bond angle deviations from ideal: 98.97 - 106.04: 74 106.04 - 113.10: 2752 113.10 - 120.16: 2219 120.16 - 127.22: 2071 127.22 - 134.29: 60 Bond angle restraints: 7176 Sorted by residual: angle pdb=" N ILE B 181 " pdb=" CA ILE B 181 " pdb=" C ILE B 181 " ideal model delta sigma weight residual 110.62 104.23 6.39 1.02e+00 9.61e-01 3.93e+01 angle pdb=" N ILE A 181 " pdb=" CA ILE A 181 " pdb=" C ILE A 181 " ideal model delta sigma weight residual 110.62 104.93 5.69 1.02e+00 9.61e-01 3.12e+01 angle pdb=" CA LEU B 121 " pdb=" C LEU B 121 " pdb=" O LEU B 121 " ideal model delta sigma weight residual 122.03 115.76 6.27 1.17e+00 7.31e-01 2.87e+01 angle pdb=" CA LEU A 121 " pdb=" C LEU A 121 " pdb=" O LEU A 121 " ideal model delta sigma weight residual 122.03 115.97 6.06 1.17e+00 7.31e-01 2.68e+01 angle pdb=" C THR B 48 " pdb=" CA THR B 48 " pdb=" CB THR B 48 " ideal model delta sigma weight residual 110.68 117.80 -7.12 1.70e+00 3.46e-01 1.76e+01 ... (remaining 7171 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.42: 2617 16.42 - 32.84: 368 32.84 - 49.26: 72 49.26 - 65.68: 25 65.68 - 82.10: 10 Dihedral angle restraints: 3092 sinusoidal: 1282 harmonic: 1810 Sorted by residual: dihedral pdb=" C LEU A 58 " pdb=" N LEU A 58 " pdb=" CA LEU A 58 " pdb=" CB LEU A 58 " ideal model delta harmonic sigma weight residual -122.60 -112.58 -10.02 0 2.50e+00 1.60e-01 1.61e+01 dihedral pdb=" C LEU B 58 " pdb=" N LEU B 58 " pdb=" CA LEU B 58 " pdb=" CB LEU B 58 " ideal model delta harmonic sigma weight residual -122.60 -112.87 -9.73 0 2.50e+00 1.60e-01 1.51e+01 dihedral pdb=" N LEU A 58 " pdb=" C LEU A 58 " pdb=" CA LEU A 58 " pdb=" CB LEU A 58 " ideal model delta harmonic sigma weight residual 122.80 113.45 9.35 0 2.50e+00 1.60e-01 1.40e+01 ... (remaining 3089 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 668 0.070 - 0.139: 77 0.139 - 0.209: 10 0.209 - 0.279: 7 0.279 - 0.349: 2 Chirality restraints: 764 Sorted by residual: chirality pdb=" CA LEU A 58 " pdb=" N LEU A 58 " pdb=" C LEU A 58 " pdb=" CB LEU A 58 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 3.04e+00 chirality pdb=" CA LEU B 58 " pdb=" N LEU B 58 " pdb=" C LEU B 58 " pdb=" CB LEU B 58 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" CA GLN A 44 " pdb=" N GLN A 44 " pdb=" C GLN A 44 " pdb=" CB GLN A 44 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 761 not shown) Planarity restraints: 892 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 46 " 0.013 2.00e-02 2.50e+03 2.59e-02 6.71e+00 pdb=" C ASN A 46 " -0.045 2.00e-02 2.50e+03 pdb=" O ASN A 46 " 0.017 2.00e-02 2.50e+03 pdb=" N CYS A 47 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 120 " 0.012 2.00e-02 2.50e+03 2.46e-02 6.06e+00 pdb=" C LEU B 120 " -0.043 2.00e-02 2.50e+03 pdb=" O LEU B 120 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU B 121 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 120 " -0.010 2.00e-02 2.50e+03 2.06e-02 4.23e+00 pdb=" C LEU A 120 " 0.036 2.00e-02 2.50e+03 pdb=" O LEU A 120 " -0.013 2.00e-02 2.50e+03 pdb=" N LEU A 121 " -0.012 2.00e-02 2.50e+03 ... (remaining 889 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 582 2.74 - 3.28: 5643 3.28 - 3.82: 8714 3.82 - 4.36: 9209 4.36 - 4.90: 15363 Nonbonded interactions: 39511 Sorted by model distance: nonbonded pdb=" NE2 GLN A 222 " pdb=" OD1 ASN A 289 " model vdw 2.199 2.520 nonbonded pdb=" NE2 GLN B 222 " pdb=" OD1 ASN B 289 " model vdw 2.200 2.520 nonbonded pdb=" ND2 ASN A 105 " pdb=" O VAL A 116 " model vdw 2.208 2.520 nonbonded pdb=" ND2 ASN B 105 " pdb=" O VAL B 116 " model vdw 2.209 2.520 nonbonded pdb=" O ILE A 183 " pdb=" NH1 ARG A 188 " model vdw 2.257 2.520 ... (remaining 39506 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' } 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: 0.610 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: 2.410 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 18.070 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5297 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 : 0.007 0.043 5314 Z= 0.443 Angle : 0.874 7.125 7176 Z= 0.568 Chirality : 0.057 0.349 764 Planarity : 0.005 0.037 892 Dihedral : 16.560 82.104 1920 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.60 % Favored : 93.07 % Rotamer: Outliers : 3.39 % Allowed : 11.96 % Favored : 84.64 % Cbeta Deviations : 0.17 % 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: -2.27 (0.30), residues: 606 helix: -1.00 (0.20), residues: 502 sheet: None (None), residues: 0 loop : -3.24 (0.57), residues: 104 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 129 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 4 residues processed: 145 average time/residue: 0.2264 time to fit residues: 39.8322 Evaluate side-chains 101 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 97 time to evaluate : 0.598 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0512 time to fit residues: 1.2425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 0.1980 chunk 45 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 24 optimal weight: 0.1980 chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 28 optimal weight: 0.0980 chunk 35 optimal weight: 0.8980 chunk 54 optimal weight: 0.5980 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN A 44 GLN A 165 ASN A 230 GLN A 334 HIS B 44 GLN B 165 ASN B 185 ASN B 241 GLN B 334 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5432 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5314 Z= 0.199 Angle : 0.664 11.660 7176 Z= 0.332 Chirality : 0.038 0.170 764 Planarity : 0.004 0.037 892 Dihedral : 4.148 16.713 666 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.96 % Allowed : 21.96 % Favored : 76.07 % 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: 0.90 (0.34), residues: 606 helix: 1.22 (0.23), residues: 512 sheet: None (None), residues: 0 loop : -2.77 (0.61), residues: 94 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 97 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 103 average time/residue: 0.1698 time to fit residues: 22.5711 Evaluate side-chains 92 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 88 time to evaluate : 0.534 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0677 time to fit residues: 1.2784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 43 optimal weight: 0.4980 chunk 53 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 HIS B 241 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5616 moved from start: 0.4398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5314 Z= 0.216 Angle : 0.632 9.549 7176 Z= 0.322 Chirality : 0.037 0.147 764 Planarity : 0.004 0.038 892 Dihedral : 4.155 16.057 666 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.14 % Allowed : 23.39 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.35), residues: 606 helix: 1.80 (0.23), residues: 516 sheet: None (None), residues: 0 loop : -3.03 (0.59), residues: 90 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 109 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 115 average time/residue: 0.2025 time to fit residues: 29.1167 Evaluate side-chains 102 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 96 time to evaluate : 0.591 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0605 time to fit residues: 1.4884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 36 optimal weight: 0.0270 chunk 54 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5662 moved from start: 0.4901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5314 Z= 0.197 Angle : 0.611 7.478 7176 Z= 0.313 Chirality : 0.038 0.153 764 Planarity : 0.004 0.038 892 Dihedral : 4.129 16.576 666 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.79 % Allowed : 24.46 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.35), residues: 606 helix: 2.02 (0.23), residues: 516 sheet: None (None), residues: 0 loop : -2.87 (0.61), residues: 90 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 109 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 1 residues processed: 115 average time/residue: 0.2028 time to fit residues: 29.1170 Evaluate side-chains 95 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 94 time to evaluate : 0.591 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0703 time to fit residues: 0.9843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 197 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5744 moved from start: 0.5712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5314 Z= 0.221 Angle : 0.653 8.470 7176 Z= 0.337 Chirality : 0.039 0.153 764 Planarity : 0.004 0.038 892 Dihedral : 4.268 18.374 666 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.86 % Allowed : 25.89 % Favored : 71.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.34), residues: 606 helix: 1.97 (0.22), residues: 514 sheet: None (None), residues: 0 loop : -2.73 (0.61), residues: 92 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 107 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 6 residues processed: 118 average time/residue: 0.2015 time to fit residues: 29.6410 Evaluate side-chains 100 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 94 time to evaluate : 0.582 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0494 time to fit residues: 1.3841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 33 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 GLN B 44 GLN B 117 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5772 moved from start: 0.6269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5314 Z= 0.232 Angle : 0.686 8.337 7176 Z= 0.349 Chirality : 0.039 0.147 764 Planarity : 0.004 0.040 892 Dihedral : 4.265 19.009 666 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.32 % Allowed : 26.96 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.34), residues: 606 helix: 1.91 (0.22), residues: 514 sheet: None (None), residues: 0 loop : -2.63 (0.62), residues: 92 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 99 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 2 residues processed: 111 average time/residue: 0.2070 time to fit residues: 28.8621 Evaluate side-chains 90 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 88 time to evaluate : 0.628 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0509 time to fit residues: 1.0836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 57 optimal weight: 0.4980 chunk 36 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 23 optimal weight: 0.0040 chunk 34 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5744 moved from start: 0.6547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5314 Z= 0.196 Angle : 0.666 9.410 7176 Z= 0.336 Chirality : 0.039 0.154 764 Planarity : 0.004 0.054 892 Dihedral : 4.217 17.878 666 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.61 % Allowed : 28.39 % Favored : 70.00 % 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: 1.99 (0.35), residues: 606 helix: 1.93 (0.22), residues: 516 sheet: None (None), residues: 0 loop : -2.37 (0.64), residues: 90 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 85 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 90 average time/residue: 0.1750 time to fit residues: 20.5031 Evaluate side-chains 87 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 81 time to evaluate : 0.557 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0536 time to fit residues: 1.3797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 52 optimal weight: 0.3980 chunk 55 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5757 moved from start: 0.6735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5314 Z= 0.205 Angle : 0.673 8.044 7176 Z= 0.340 Chirality : 0.039 0.172 764 Planarity : 0.004 0.058 892 Dihedral : 4.239 17.752 666 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.89 % Allowed : 28.57 % Favored : 70.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.34), residues: 606 helix: 1.91 (0.22), residues: 514 sheet: None (None), residues: 0 loop : -2.37 (0.63), residues: 92 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 76 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 79 average time/residue: 0.1712 time to fit residues: 17.8897 Evaluate side-chains 80 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 77 time to evaluate : 0.590 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0475 time to fit residues: 1.0208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 56 optimal weight: 0.2980 chunk 34 optimal weight: 0.7980 chunk 27 optimal weight: 0.4980 chunk 39 optimal weight: 0.0170 chunk 59 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5736 moved from start: 0.6909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5314 Z= 0.182 Angle : 0.663 8.397 7176 Z= 0.330 Chirality : 0.038 0.166 764 Planarity : 0.004 0.060 892 Dihedral : 4.150 17.083 666 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.71 % Allowed : 28.57 % Favored : 70.71 % 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: 2.06 (0.34), residues: 606 helix: 1.96 (0.22), residues: 516 sheet: None (None), residues: 0 loop : -2.27 (0.65), residues: 90 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 92 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 96 average time/residue: 0.2043 time to fit residues: 25.0669 Evaluate side-chains 88 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.620 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 0.9980 chunk 36 optimal weight: 0.0000 chunk 29 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5763 moved from start: 0.7141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5314 Z= 0.208 Angle : 0.693 8.457 7176 Z= 0.350 Chirality : 0.039 0.176 764 Planarity : 0.005 0.061 892 Dihedral : 4.187 17.551 666 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.18 % Allowed : 29.64 % Favored : 70.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.35), residues: 606 helix: 1.87 (0.23), residues: 516 sheet: None (None), residues: 0 loop : -2.16 (0.66), residues: 90 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 81 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 82 average time/residue: 0.1649 time to fit residues: 18.2612 Evaluate side-chains 80 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 79 time to evaluate : 0.588 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0514 time to fit residues: 0.9403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 1.9990 chunk 6 optimal weight: 0.2980 chunk 8 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 38 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 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 = 0.4798 r_free = 0.4798 target = 0.260128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4615 r_free = 0.4615 target = 0.240458 restraints weight = 7750.343| |-----------------------------------------------------------------------------| r_work (start): 0.4645 rms_B_bonded: 1.80 r_work: 0.4567 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work (final): 0.4567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6058 moved from start: 0.7305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5314 Z= 0.215 Angle : 0.705 8.446 7176 Z= 0.354 Chirality : 0.039 0.187 764 Planarity : 0.005 0.062 892 Dihedral : 4.206 17.264 666 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.00 % Allowed : 29.64 % Favored : 70.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.35), residues: 606 helix: 1.84 (0.22), residues: 516 sheet: None (None), residues: 0 loop : -2.10 (0.67), residues: 90 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1405.30 seconds wall clock time: 25 minutes 59.92 seconds (1559.92 seconds total)