Starting phenix.real_space_refine (version: dev) on Tue Nov 29 11:34:48 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usb_26731/11_2022/7usb_26731.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usb_26731/11_2022/7usb_26731.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usb_26731/11_2022/7usb_26731.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usb_26731/11_2022/7usb_26731.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usb_26731/11_2022/7usb_26731.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usb_26731/11_2022/7usb_26731.pdb" } resolution = 3.1 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= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 152": "OD1" <-> "OD2" Residue "A ARG 154": "NH1" <-> "NH2" Residue "A PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 1661 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1591 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 202} Chain breaks: 5 Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 185 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 5, 'TYR:plan': 1, 'ASN:plan1': 5, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 84 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 1.61, per 1000 atoms: 0.97 Number of scatterers: 1661 At special positions: 0 Unit cell: (57.324, 67.44, 57.324, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 12 16.00 O 292 8.00 N 279 7.00 C 1078 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 21 " - pdb=" SG CYS A 68 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 147 " distance=2.04 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 153 " distance=2.03 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 170 " distance=2.04 Simple disulfide: pdb=" SG CYS A 250 " - pdb=" SG CYS A 254 " distance=2.13 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG A5401 " - " ASN A 242 " " NAG A5402 " - " ASN A 26 " " NAG A5403 " - " ASN A 42 " " NAG B 1 " - " ASN A 249 " Time building additional restraints: 0.79 Conformation dependent library (CDL) restraints added in 255.5 milliseconds 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 404 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 4 sheets defined 13.6% alpha, 33.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 29 through 32 Processing helix chain 'A' and resid 33 through 44 Processing helix chain 'A' and resid 45 through 47 No H-bonds generated for 'chain 'A' and resid 45 through 47' Processing helix chain 'A' and resid 162 through 166 Processing helix chain 'A' and resid 254 through 258 Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 27 Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 57 Processing sheet with id=AA3, first strand: chain 'A' and resid 78 through 80 removed outlier: 7.297A pdb=" N PHE A 202 " --> pdb=" O LYS A 110 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N LYS A 110 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N THR A 204 " --> pdb=" O LYS A 108 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE A 130 " --> pdb=" O LEU A 155 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU A 155 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ILE A 132 " --> pdb=" O CYS A 153 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N CYS A 153 " --> pdb=" O ILE A 132 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 191 through 196 64 hydrogen bonds defined for protein. 150 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.42 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 390 1.33 - 1.46: 470 1.46 - 1.58: 830 1.58 - 1.71: 1 1.71 - 1.84: 14 Bond restraints: 1705 Sorted by residual: bond pdb=" C5 NAG A5401 " pdb=" O5 NAG A5401 " ideal model delta sigma weight residual 1.435 1.478 -0.043 1.10e-02 8.26e+03 1.54e+01 bond pdb=" C5 NAG A5402 " pdb=" O5 NAG A5402 " ideal model delta sigma weight residual 1.435 1.475 -0.040 1.10e-02 8.26e+03 1.33e+01 bond pdb=" CB LEU A 207 " pdb=" CG LEU A 207 " ideal model delta sigma weight residual 1.530 1.602 -0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" C3 NAG B 1 " pdb=" C4 NAG B 1 " ideal model delta sigma weight residual 1.523 1.559 -0.036 1.00e-02 1.00e+04 1.27e+01 bond pdb=" CA PRO A 48 " pdb=" C PRO A 48 " ideal model delta sigma weight residual 1.514 1.534 -0.019 5.50e-03 3.31e+04 1.23e+01 ... (remaining 1700 not shown) Histogram of bond angle deviations from ideal: 100.64 - 107.29: 83 107.29 - 113.94: 891 113.94 - 120.59: 714 120.59 - 127.24: 617 127.24 - 133.89: 32 Bond angle restraints: 2337 Sorted by residual: angle pdb=" CD1 LEU A 41 " pdb=" CG LEU A 41 " pdb=" CD2 LEU A 41 " ideal model delta sigma weight residual 110.80 133.28 -22.48 2.20e+00 2.07e-01 1.04e+02 angle pdb=" C LEU A 47 " pdb=" N PRO A 48 " pdb=" CA PRO A 48 " ideal model delta sigma weight residual 119.66 127.07 -7.41 7.30e-01 1.88e+00 1.03e+02 angle pdb=" CG1 VAL A 185 " pdb=" CB VAL A 185 " pdb=" CG2 VAL A 185 " ideal model delta sigma weight residual 110.80 131.09 -20.29 2.20e+00 2.07e-01 8.50e+01 angle pdb=" C PRO A 48 " pdb=" N PRO A 49 " pdb=" CA PRO A 49 " ideal model delta sigma weight residual 119.56 127.28 -7.72 1.01e+00 9.80e-01 5.84e+01 angle pdb=" C PRO A 137 " pdb=" N PRO A 138 " pdb=" CA PRO A 138 " ideal model delta sigma weight residual 120.03 126.02 -5.99 9.90e-01 1.02e+00 3.67e+01 ... (remaining 2332 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 922 17.81 - 35.63: 34 35.63 - 53.44: 7 53.44 - 71.25: 6 71.25 - 89.07: 1 Dihedral angle restraints: 970 sinusoidal: 347 harmonic: 623 Sorted by residual: dihedral pdb=" CB CYS A 21 " pdb=" SG CYS A 21 " pdb=" SG CYS A 68 " pdb=" CB CYS A 68 " ideal model delta sinusoidal sigma weight residual 93.00 162.97 -69.97 1 1.00e+01 1.00e-02 6.31e+01 dihedral pdb=" CB CYS A 250 " pdb=" SG CYS A 250 " pdb=" SG CYS A 254 " pdb=" CB CYS A 254 " ideal model delta sinusoidal sigma weight residual 93.00 153.68 -60.68 1 1.00e+01 1.00e-02 4.90e+01 dihedral pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " pdb=" SG CYS A 147 " pdb=" CB CYS A 147 " ideal model delta sinusoidal sigma weight residual -86.00 -142.30 56.30 1 1.00e+01 1.00e-02 4.27e+01 ... (remaining 967 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.109: 226 0.109 - 0.216: 37 0.216 - 0.323: 4 0.323 - 0.430: 7 0.430 - 0.537: 2 Chirality restraints: 276 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.50 0.10 2.00e-02 2.50e+03 2.73e+01 chirality pdb=" CG LEU A 41 " pdb=" CB LEU A 41 " pdb=" CD1 LEU A 41 " pdb=" CD2 LEU A 41 " both_signs ideal model delta sigma weight residual False -2.59 -2.05 -0.54 2.00e-01 2.50e+01 7.21e+00 chirality pdb=" CB VAL A 185 " pdb=" CA VAL A 185 " pdb=" CG1 VAL A 185 " pdb=" CG2 VAL A 185 " both_signs ideal model delta sigma weight residual False -2.63 -2.10 -0.52 2.00e-01 2.50e+01 6.87e+00 ... (remaining 273 not shown) Planarity restraints: 293 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A5403 " -0.211 2.00e-02 2.50e+03 1.79e-01 4.01e+02 pdb=" C7 NAG A5403 " 0.043 2.00e-02 2.50e+03 pdb=" C8 NAG A5403 " 0.037 2.00e-02 2.50e+03 pdb=" N2 NAG A5403 " 0.294 2.00e-02 2.50e+03 pdb=" O7 NAG A5403 " -0.163 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 2 " 0.103 2.00e-02 2.50e+03 8.70e-02 9.46e+01 pdb=" C7 NAG B 2 " -0.020 2.00e-02 2.50e+03 pdb=" C8 NAG B 2 " -0.028 2.00e-02 2.50e+03 pdb=" N2 NAG B 2 " -0.138 2.00e-02 2.50e+03 pdb=" O7 NAG B 2 " 0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 133 " -0.021 2.00e-02 2.50e+03 4.13e-02 1.70e+01 pdb=" C CYS A 133 " 0.071 2.00e-02 2.50e+03 pdb=" O CYS A 133 " -0.027 2.00e-02 2.50e+03 pdb=" N LYS A 134 " -0.024 2.00e-02 2.50e+03 ... (remaining 290 not shown) Histogram of nonbonded interaction distances: 2.59 - 3.05: 931 3.05 - 3.51: 1400 3.51 - 3.98: 2544 3.98 - 4.44: 2901 4.44 - 4.90: 4618 Nonbonded interactions: 12394 Sorted by model distance: nonbonded pdb=" N GLY A 243 " pdb=" N THR A 244 " model vdw 2.590 2.560 nonbonded pdb=" N PHE A 202 " pdb=" O PHE A 202 " model vdw 2.614 2.496 nonbonded pdb=" O LYS A 110 " pdb=" CD PRO A 111 " model vdw 2.626 2.752 nonbonded pdb=" OD1 ASP A 89 " pdb=" N TYR A 90 " model vdw 2.634 2.520 nonbonded pdb=" N GLN A 167 " pdb=" O GLN A 167 " model vdw 2.647 2.496 ... (remaining 12389 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 12 5.16 5 C 1078 2.51 5 N 279 2.21 5 O 292 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 25.430 Check model and map are aligned: 0.020 Convert atoms to be neutral: 0.040 Process input model: 12.320 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 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 : 0.012 0.072 1705 Z= 0.804 Angle : 1.701 22.477 2337 Z= 1.076 Chirality : 0.106 0.537 276 Planarity : 0.013 0.179 289 Dihedral : 10.613 89.066 551 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer Outliers : 1.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.28 (0.53), residues: 201 helix: -1.80 (0.97), residues: 18 sheet: 1.28 (0.53), residues: 75 loop : -1.01 (0.52), residues: 108 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 33 time to evaluate : 0.187 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 35 average time/residue: 0.1031 time to fit residues: 4.3860 Evaluate side-chains 18 residues out of total 194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 17 time to evaluate : 0.192 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0217 time to fit residues: 0.3012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 17 optimal weight: 0.6980 chunk 15 optimal weight: 0.4980 chunk 8 optimal weight: 0.3980 chunk 5 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 6 optimal weight: 0.0970 chunk 12 optimal weight: 0.4980 chunk 19 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN A 148 ASN A 169 ASN A 172 ASN A 240 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.037 1705 Z= 0.408 Angle : 0.694 5.206 2337 Z= 0.387 Chirality : 0.050 0.237 276 Planarity : 0.005 0.033 289 Dihedral : 5.945 18.239 255 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer Outliers : 2.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.65 (0.55), residues: 201 helix: 0.79 (1.39), residues: 13 sheet: 0.64 (0.56), residues: 76 loop : -1.41 (0.52), residues: 112 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 22 time to evaluate : 0.191 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 25 average time/residue: 0.1554 time to fit residues: 4.5364 Evaluate side-chains 20 residues out of total 194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 18 time to evaluate : 0.193 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0218 time to fit residues: 0.3329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 6 optimal weight: 0.8980 chunk 15 optimal weight: 0.0970 chunk 18 optimal weight: 0.4980 chunk 14 optimal weight: 0.2980 chunk 9 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 19 optimal weight: 0.3980 chunk 20 optimal weight: 0.4980 chunk 10 optimal weight: 0.5980 chunk 5 optimal weight: 0.4980 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.033 1705 Z= 0.331 Angle : 0.603 4.891 2337 Z= 0.332 Chirality : 0.050 0.230 276 Planarity : 0.004 0.035 289 Dihedral : 5.623 16.770 255 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer Outliers : 1.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.56), residues: 201 helix: 0.83 (1.31), residues: 13 sheet: 0.36 (0.60), residues: 73 loop : -1.74 (0.52), residues: 115 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 19 time to evaluate : 0.194 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 20 average time/residue: 0.1273 time to fit residues: 3.1325 Evaluate side-chains 20 residues out of total 194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 18 time to evaluate : 0.191 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0199 time to fit residues: 0.3298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 16 optimal weight: 0.4980 chunk 11 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 15 optimal weight: 0.3980 chunk 8 optimal weight: 0.3980 chunk 17 optimal weight: 0.0970 chunk 14 optimal weight: 0.2980 chunk 10 optimal weight: 0.7980 chunk 18 optimal weight: 0.0980 chunk 5 optimal weight: 0.5980 chunk 6 optimal weight: 0.0970 overall best weight: 0.1976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 1705 Z= 0.216 Angle : 0.528 4.779 2337 Z= 0.290 Chirality : 0.047 0.247 276 Planarity : 0.003 0.032 289 Dihedral : 5.409 15.568 255 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.09 (0.57), residues: 201 helix: 0.82 (1.27), residues: 13 sheet: 0.26 (0.61), residues: 73 loop : -1.64 (0.54), residues: 115 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 21 time to evaluate : 0.199 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 21 average time/residue: 0.1301 time to fit residues: 3.3295 Evaluate side-chains 20 residues out of total 194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 19 time to evaluate : 0.192 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0190 time to fit residues: 0.2816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 18 optimal weight: 0.4980 chunk 4 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 1 optimal weight: 0.0870 chunk 6 optimal weight: 0.4980 chunk 10 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.032 1705 Z= 0.405 Angle : 0.620 6.125 2337 Z= 0.336 Chirality : 0.052 0.256 276 Planarity : 0.004 0.036 289 Dihedral : 5.743 16.686 255 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer Outliers : 2.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.42 (0.57), residues: 201 helix: 0.57 (1.28), residues: 13 sheet: -0.01 (0.62), residues: 73 loop : -1.84 (0.55), residues: 115 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 23 time to evaluate : 0.170 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 24 average time/residue: 0.1478 time to fit residues: 4.1751 Evaluate side-chains 23 residues out of total 194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 20 time to evaluate : 0.204 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0272 time to fit residues: 0.3950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 2 optimal weight: 0.0670 chunk 11 optimal weight: 0.9990 chunk 14 optimal weight: 0.3980 chunk 17 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 12 optimal weight: 0.1980 chunk 9 optimal weight: 0.7980 chunk 8 optimal weight: 0.0970 chunk 6 optimal weight: 0.1980 chunk 3 optimal weight: 0.1980 chunk 13 optimal weight: 0.9990 overall best weight: 0.1516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.084 1705 Z= 0.274 Angle : 0.561 6.315 2337 Z= 0.311 Chirality : 0.048 0.255 276 Planarity : 0.003 0.030 289 Dihedral : 5.713 25.112 255 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer Outliers : 2.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.56 (0.55), residues: 201 helix: 0.79 (1.33), residues: 13 sheet: -0.12 (0.60), residues: 72 loop : -1.95 (0.51), residues: 116 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 24 time to evaluate : 0.186 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 26 average time/residue: 0.1425 time to fit residues: 4.3746 Evaluate side-chains 24 residues out of total 194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 21 time to evaluate : 0.188 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1493 time to fit residues: 0.7470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 10 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 18 optimal weight: 0.4980 chunk 19 optimal weight: 0.4980 chunk 17 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 8 optimal weight: 0.0870 chunk 14 optimal weight: 0.0670 chunk 5 optimal weight: 0.3980 chunk 12 optimal weight: 0.0980 overall best weight: 0.2296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 1705 Z= 0.269 Angle : 0.549 5.366 2337 Z= 0.300 Chirality : 0.048 0.249 276 Planarity : 0.003 0.030 289 Dihedral : 5.937 37.966 255 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer Outliers : 1.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.51 % 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: -1.54 (0.56), residues: 201 helix: 0.75 (1.32), residues: 13 sheet: -0.18 (0.61), residues: 72 loop : -1.86 (0.52), residues: 116 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 23 time to evaluate : 0.189 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 23 average time/residue: 0.1493 time to fit residues: 4.0466 Evaluate side-chains 24 residues out of total 194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 23 time to evaluate : 0.205 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0199 time to fit residues: 0.2744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 19 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 0.2980 chunk 20 optimal weight: 0.0020 chunk 16 optimal weight: 0.3980 chunk 1 optimal weight: 0.4980 chunk 10 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 15 optimal weight: 0.1980 overall best weight: 0.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.4214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 1705 Z= 0.281 Angle : 0.565 4.677 2337 Z= 0.307 Chirality : 0.049 0.255 276 Planarity : 0.004 0.030 289 Dihedral : 5.729 32.385 255 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.51 % 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: -1.48 (0.56), residues: 201 helix: 0.73 (1.33), residues: 13 sheet: -0.15 (0.61), residues: 72 loop : -1.81 (0.52), residues: 116 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 24 time to evaluate : 0.177 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 24 average time/residue: 0.1451 time to fit residues: 4.0921 Evaluate side-chains 25 residues out of total 194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 24 time to evaluate : 0.200 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0392 time to fit residues: 0.3155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 2 optimal weight: 0.0000 chunk 4 optimal weight: 0.0870 chunk 16 optimal weight: 0.5980 chunk 6 optimal weight: 0.0270 chunk 17 optimal weight: 0.8980 chunk 3 optimal weight: 0.0570 chunk 14 optimal weight: 0.3980 chunk 0 optimal weight: 0.4980 chunk 12 optimal weight: 0.1980 chunk 19 optimal weight: 0.0980 chunk 11 optimal weight: 0.7980 overall best weight: 0.0538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.4252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 1705 Z= 0.148 Angle : 0.484 4.876 2337 Z= 0.268 Chirality : 0.046 0.239 276 Planarity : 0.003 0.026 289 Dihedral : 5.314 29.461 255 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.38 (0.55), residues: 201 helix: 0.99 (1.37), residues: 13 sheet: -0.14 (0.60), residues: 72 loop : -1.72 (0.52), residues: 116 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 26 time to evaluate : 0.192 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 26 average time/residue: 0.1425 time to fit residues: 4.3938 Evaluate side-chains 25 residues out of total 194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 24 time to evaluate : 0.193 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0434 time to fit residues: 0.3251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 14 optimal weight: 0.7980 chunk 0 optimal weight: 0.9990 chunk 13 optimal weight: 0.0980 chunk 12 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 3 optimal weight: 0.2980 chunk 2 optimal weight: 0.2980 chunk 4 optimal weight: 0.3980 chunk 16 optimal weight: 0.1980 overall best weight: 0.2580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.4372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 1705 Z= 0.260 Angle : 0.545 4.859 2337 Z= 0.295 Chirality : 0.048 0.237 276 Planarity : 0.003 0.027 289 Dihedral : 5.567 30.699 255 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.51 % 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: -1.61 (0.55), residues: 201 helix: -0.43 (1.18), residues: 19 sheet: -0.21 (0.60), residues: 72 loop : -1.83 (0.53), residues: 110 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.181 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.1587 time to fit residues: 4.0897 Evaluate side-chains 22 residues out of total 194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.185 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 19 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 4 optimal weight: 0.0870 chunk 13 optimal weight: 0.0870 chunk 7 optimal weight: 0.8980 chunk 3 optimal weight: 0.2980 chunk 10 optimal weight: 0.8980 chunk 20 optimal weight: 0.0050 overall best weight: 0.2150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 189 HIS ** 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 = 0.3977 r_free = 0.3977 target = 0.174585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.145390 restraints weight = 1927.098| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.44 r_work: 0.3619 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3606 rms_B_bonded: 2.17 restraints_weight: 0.2500 r_work: 0.3590 rms_B_bonded: 2.25 restraints_weight: 0.1250 r_work: 0.3574 rms_B_bonded: 2.40 restraints_weight: 0.0625 r_work: 0.3554 rms_B_bonded: 2.63 restraints_weight: 0.0312 r_work: 0.3531 rms_B_bonded: 2.95 restraints_weight: 0.0156 r_work: 0.3504 rms_B_bonded: 3.37 restraints_weight: 0.0078 r_work: 0.3471 rms_B_bonded: 3.92 restraints_weight: 0.0039 r_work: 0.3431 rms_B_bonded: 4.65 restraints_weight: 0.0020 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.4414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 1705 Z= 0.225 Angle : 0.520 4.714 2337 Z= 0.283 Chirality : 0.047 0.244 276 Planarity : 0.003 0.027 289 Dihedral : 5.508 29.505 255 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.64 (0.55), residues: 201 helix: -0.38 (1.20), residues: 19 sheet: -0.29 (0.59), residues: 72 loop : -1.82 (0.53), residues: 110 =============================================================================== Job complete usr+sys time: 1286.44 seconds wall clock time: 23 minutes 22.22 seconds (1402.22 seconds total)