Starting phenix.real_space_refine (version: dev) on Tue Nov 29 11:48:35 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzu_24778/11_2022/7rzu_24778.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzu_24778/11_2022/7rzu_24778.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzu_24778/11_2022/7rzu_24778.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzu_24778/11_2022/7rzu_24778.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzu_24778/11_2022/7rzu_24778.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzu_24778/11_2022/7rzu_24778.pdb" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 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 None 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: 2439 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 532 Classifications: {'peptide': 71} Link IDs: {'TRANS': 70} Chain: "B" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 532 Classifications: {'peptide': 71} Link IDs: {'TRANS': 70} Chain: "C" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 532 Classifications: {'peptide': 71} Link IDs: {'TRANS': 70} Chain: "D" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 281 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "E" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 281 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "F" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 281 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Time building chain proxies: 1.69, per 1000 atoms: 0.69 Number of scatterers: 2439 At special positions: 0 Unit cell: (44.8938, 51.4238, 116.724, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 513 8.00 N 426 7.00 C 1500 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: 1.05 Conformation dependent library (CDL) restraints added in 419.5 milliseconds 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 618 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 0 sheets defined 82.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing helix chain 'A' and resid 918 through 988 removed outlier: 3.521A pdb=" N GLU A 988 " --> pdb=" O LEU A 984 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 988 removed outlier: 3.522A pdb=" N GLU B 988 " --> pdb=" O LEU B 984 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 988 removed outlier: 3.521A pdb=" N GLU C 988 " --> pdb=" O LEU C 984 " (cutoff:3.500A) Processing helix chain 'D' and resid 1179 through 1193 Processing helix chain 'D' and resid 1194 through 1197 removed outlier: 3.675A pdb=" N LEU D1197 " --> pdb=" O ASN D1194 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1194 through 1197' Processing helix chain 'E' and resid 1179 through 1193 Processing helix chain 'E' and resid 1194 through 1197 removed outlier: 3.676A pdb=" N LEU E1197 " --> pdb=" O ASN E1194 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1194 through 1197' Processing helix chain 'F' and resid 1179 through 1193 Processing helix chain 'F' and resid 1194 through 1197 removed outlier: 3.676A pdb=" N LEU F1197 " --> pdb=" O ASN F1194 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 1194 through 1197' 229 hydrogen bonds defined for protein. 687 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: 0.59 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 465 1.29 - 1.35: 399 1.35 - 1.42: 48 1.42 - 1.48: 366 1.48 - 1.54: 1161 Bond restraints: 2439 Sorted by residual: bond pdb=" N ILE D1179 " pdb=" CA ILE D1179 " ideal model delta sigma weight residual 1.459 1.449 0.010 1.25e-02 6.40e+03 6.75e-01 bond pdb=" C ILE E1179 " pdb=" O ILE E1179 " ideal model delta sigma weight residual 1.236 1.226 0.010 1.19e-02 7.06e+03 6.73e-01 bond pdb=" C ILE D1179 " pdb=" O ILE D1179 " ideal model delta sigma weight residual 1.236 1.227 0.010 1.19e-02 7.06e+03 6.49e-01 bond pdb=" C ILE F1179 " pdb=" O ILE F1179 " ideal model delta sigma weight residual 1.236 1.227 0.010 1.19e-02 7.06e+03 6.41e-01 bond pdb=" N ILE E1179 " pdb=" CA ILE E1179 " ideal model delta sigma weight residual 1.459 1.449 0.010 1.25e-02 6.40e+03 5.93e-01 ... (remaining 2434 not shown) Histogram of bond angle deviations from ideal: 106.65 - 110.22: 335 110.22 - 113.78: 1198 113.78 - 117.34: 301 117.34 - 120.90: 905 120.90 - 124.47: 549 Bond angle restraints: 3288 Sorted by residual: angle pdb=" CA LEU A 984 " pdb=" CB LEU A 984 " pdb=" CG LEU A 984 " ideal model delta sigma weight residual 116.30 123.66 -7.36 3.50e+00 8.16e-02 4.42e+00 angle pdb=" CA LEU B 984 " pdb=" CB LEU B 984 " pdb=" CG LEU B 984 " ideal model delta sigma weight residual 116.30 123.65 -7.35 3.50e+00 8.16e-02 4.40e+00 angle pdb=" CA LEU C 984 " pdb=" CB LEU C 984 " pdb=" CG LEU C 984 " ideal model delta sigma weight residual 116.30 123.64 -7.34 3.50e+00 8.16e-02 4.40e+00 angle pdb=" C SER B 982 " pdb=" N ARG B 983 " pdb=" CA ARG B 983 " ideal model delta sigma weight residual 120.44 117.62 2.82 1.36e+00 5.41e-01 4.31e+00 angle pdb=" C SER C 982 " pdb=" N ARG C 983 " pdb=" CA ARG C 983 " ideal model delta sigma weight residual 120.44 117.62 2.82 1.36e+00 5.41e-01 4.31e+00 ... (remaining 3283 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 1413 17.83 - 35.65: 96 35.65 - 53.48: 9 53.48 - 71.30: 9 71.30 - 89.13: 3 Dihedral angle restraints: 1530 sinusoidal: 594 harmonic: 936 Sorted by residual: dihedral pdb=" CA ARG B 983 " pdb=" C ARG B 983 " pdb=" N LEU B 984 " pdb=" CA LEU B 984 " ideal model delta harmonic sigma weight residual 180.00 160.29 19.71 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA ARG A 983 " pdb=" C ARG A 983 " pdb=" N LEU A 984 " pdb=" CA LEU A 984 " ideal model delta harmonic sigma weight residual 180.00 160.32 19.68 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA ARG C 983 " pdb=" C ARG C 983 " pdb=" N LEU C 984 " pdb=" CA LEU C 984 " ideal model delta harmonic sigma weight residual 180.00 160.37 19.63 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 1527 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 332 0.042 - 0.084: 73 0.084 - 0.125: 9 0.125 - 0.167: 0 0.167 - 0.209: 3 Chirality restraints: 417 Sorted by residual: chirality pdb=" CG LEU A 984 " pdb=" CB LEU A 984 " pdb=" CD1 LEU A 984 " pdb=" CD2 LEU A 984 " both_signs ideal model delta sigma weight residual False -2.59 -2.80 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CG LEU B 984 " pdb=" CB LEU B 984 " pdb=" CD1 LEU B 984 " pdb=" CD2 LEU B 984 " both_signs ideal model delta sigma weight residual False -2.59 -2.80 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CG LEU C 984 " pdb=" CB LEU C 984 " pdb=" CD1 LEU C 984 " pdb=" CD2 LEU C 984 " both_signs ideal model delta sigma weight residual False -2.59 -2.79 0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 414 not shown) Planarity restraints: 432 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 983 " -0.196 9.50e-02 1.11e+02 8.78e-02 4.80e+00 pdb=" NE ARG C 983 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG C 983 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG C 983 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 983 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 983 " -0.194 9.50e-02 1.11e+02 8.72e-02 4.73e+00 pdb=" NE ARG B 983 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG B 983 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG B 983 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 983 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 983 " -0.194 9.50e-02 1.11e+02 8.71e-02 4.72e+00 pdb=" NE ARG A 983 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 983 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 983 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 983 " -0.005 2.00e-02 2.50e+03 ... (remaining 429 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 423 2.75 - 3.29: 2544 3.29 - 3.82: 4286 3.82 - 4.36: 4758 4.36 - 4.90: 8146 Nonbonded interactions: 20157 Sorted by model distance: nonbonded pdb=" O LEU A 984 " pdb=" NH2 ARG B 983 " model vdw 2.212 2.520 nonbonded pdb=" O LEU B 984 " pdb=" NH2 ARG C 983 " model vdw 2.214 2.520 nonbonded pdb=" NH2 ARG A 983 " pdb=" O LEU C 984 " model vdw 2.234 2.520 nonbonded pdb=" NE2 GLN C 965 " pdb=" O ASP E1168 " model vdw 2.316 2.520 nonbonded pdb=" NE2 GLN B 965 " pdb=" O ASP D1168 " model vdw 2.334 2.520 ... (remaining 20152 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 3 Type Number sf(0) Gaussians C 1500 2.51 5 N 426 2.21 5 O 513 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: 0.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.420 Check model and map are aligned: 0.040 Convert atoms to be neutral: 0.020 Process input model: 11.420 Find NCS groups from input model: 0.140 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:13.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.023 2439 Z= 0.381 Angle : 0.505 7.356 3288 Z= 0.280 Chirality : 0.039 0.209 417 Planarity : 0.008 0.088 432 Dihedral : 13.614 89.129 912 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.45), residues: 312 helix: 1.78 (0.30), residues: 246 sheet: None (None), residues: 0 loop : -1.39 (0.82), residues: 66 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.6232 time to fit residues: 23.5377 Evaluate side-chains 35 residues out of total 285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.278 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 27 optimal weight: 0.4980 chunk 8 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1173 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.026 2439 Z= 0.226 Angle : 0.474 10.116 3288 Z= 0.226 Chirality : 0.034 0.136 417 Planarity : 0.002 0.017 432 Dihedral : 3.353 11.844 324 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 2.11 % 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: 4.20 (0.46), residues: 312 helix: 3.61 (0.29), residues: 243 sheet: None (None), residues: 0 loop : -0.59 (0.80), residues: 69 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 30 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 34 average time/residue: 0.6310 time to fit residues: 22.5808 Evaluate side-chains 35 residues out of total 285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 31 time to evaluate : 0.274 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.0247 time to fit residues: 0.4434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1173 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.022 2439 Z= 0.252 Angle : 0.444 9.264 3288 Z= 0.213 Chirality : 0.033 0.111 417 Planarity : 0.003 0.028 432 Dihedral : 3.147 10.212 324 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 3.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.81 (0.44), residues: 312 helix: 3.98 (0.28), residues: 246 sheet: None (None), residues: 0 loop : -0.30 (0.81), residues: 66 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 32 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 35 average time/residue: 0.6281 time to fit residues: 23.1098 Evaluate side-chains 38 residues out of total 285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 32 time to evaluate : 0.275 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 3 residues processed: 3 average time/residue: 0.0796 time to fit residues: 0.6681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 27 optimal weight: 0.1980 chunk 28 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1173 ASN E1180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.018 2439 Z= 0.222 Angle : 0.402 8.844 3288 Z= 0.198 Chirality : 0.032 0.106 417 Planarity : 0.002 0.020 432 Dihedral : 3.063 9.300 324 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 2.81 % 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: 5.00 (0.44), residues: 312 helix: 4.19 (0.27), residues: 243 sheet: None (None), residues: 0 loop : -0.36 (0.76), residues: 69 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 31 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 7 residues processed: 33 average time/residue: 0.6491 time to fit residues: 22.5200 Evaluate side-chains 38 residues out of total 285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 31 time to evaluate : 0.244 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 3 residues processed: 5 average time/residue: 0.3354 time to fit residues: 2.1349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 0.0050 chunk 11 optimal weight: 0.5980 chunk 24 optimal weight: 0.0870 chunk 20 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 overall best weight: 0.3772 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1173 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.022 2439 Z= 0.160 Angle : 0.405 9.258 3288 Z= 0.195 Chirality : 0.031 0.107 417 Planarity : 0.002 0.016 432 Dihedral : 2.964 9.291 324 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 3.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.21 (0.44), residues: 312 helix: 4.37 (0.27), residues: 243 sheet: None (None), residues: 0 loop : -0.42 (0.73), residues: 69 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 31 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 35 average time/residue: 0.6146 time to fit residues: 22.6698 Evaluate side-chains 37 residues out of total 285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 31 time to evaluate : 0.271 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 4 residues processed: 3 average time/residue: 0.5525 time to fit residues: 2.1364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 24 optimal weight: 0.0010 chunk 13 optimal weight: 0.6980 chunk 2 optimal weight: 0.4980 chunk 9 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 27 optimal weight: 0.0980 chunk 3 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 overall best weight: 0.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1173 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 2439 Z= 0.167 Angle : 0.485 12.650 3288 Z= 0.230 Chirality : 0.031 0.107 417 Planarity : 0.004 0.071 432 Dihedral : 3.020 10.988 324 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 3.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.34 (0.43), residues: 312 helix: 4.47 (0.27), residues: 243 sheet: None (None), residues: 0 loop : -0.36 (0.74), residues: 69 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 33 time to evaluate : 0.275 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 37 average time/residue: 0.5038 time to fit residues: 19.8285 Evaluate side-chains 39 residues out of total 285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 33 time to evaluate : 0.281 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 4 residues processed: 3 average time/residue: 0.1223 time to fit residues: 0.8346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 11 optimal weight: 0.1980 chunk 8 optimal weight: 0.2980 chunk 5 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 14 optimal weight: 0.0980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1173 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 2439 Z= 0.162 Angle : 0.479 9.630 3288 Z= 0.221 Chirality : 0.031 0.107 417 Planarity : 0.003 0.042 432 Dihedral : 2.954 8.165 324 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 3.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.46 (0.43), residues: 312 helix: 4.58 (0.26), residues: 243 sheet: None (None), residues: 0 loop : -0.45 (0.70), residues: 69 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 35 time to evaluate : 0.253 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 39 average time/residue: 0.5198 time to fit residues: 21.5965 Evaluate side-chains 41 residues out of total 285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 35 time to evaluate : 0.254 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 2 residues processed: 4 average time/residue: 0.4031 time to fit residues: 2.0753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 0.0970 chunk 22 optimal weight: 0.9980 chunk 26 optimal weight: 0.2980 chunk 27 optimal weight: 0.0470 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 8 optimal weight: 0.2980 chunk 24 optimal weight: 0.8980 chunk 17 optimal weight: 0.3980 overall best weight: 0.2276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 965 GLN ** B 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1173 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 2439 Z= 0.131 Angle : 0.457 9.282 3288 Z= 0.219 Chirality : 0.031 0.107 417 Planarity : 0.002 0.012 432 Dihedral : 2.872 9.234 324 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 1.75 % 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: 5.58 (0.43), residues: 312 helix: 4.66 (0.26), residues: 243 sheet: None (None), residues: 0 loop : -0.38 (0.69), residues: 69 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 37 time to evaluate : 0.287 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 39 average time/residue: 0.5142 time to fit residues: 21.3146 Evaluate side-chains 39 residues out of total 285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 36 time to evaluate : 0.242 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 0.0819 time to fit residues: 0.5352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 chunk 27 optimal weight: 0.0000 chunk 23 optimal weight: 0.6980 chunk 2 optimal weight: 0.4980 chunk 18 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 955 ASN ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1173 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 2439 Z= 0.195 Angle : 0.463 8.696 3288 Z= 0.227 Chirality : 0.032 0.108 417 Planarity : 0.002 0.019 432 Dihedral : 2.979 8.360 324 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 0.70 % 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: 5.37 (0.43), residues: 312 helix: 4.51 (0.27), residues: 243 sheet: None (None), residues: 0 loop : -0.45 (0.68), residues: 69 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 34 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 36 average time/residue: 0.5250 time to fit residues: 20.0030 Evaluate side-chains 36 residues out of total 285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 34 time to evaluate : 0.245 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.3571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 0.4980 chunk 21 optimal weight: 0.9980 chunk 3 optimal weight: 0.4980 chunk 6 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 17 optimal weight: 0.4980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1173 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 2439 Z= 0.221 Angle : 0.466 8.571 3288 Z= 0.232 Chirality : 0.033 0.107 417 Planarity : 0.002 0.014 432 Dihedral : 3.082 8.765 324 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 1.75 % 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: 5.19 (0.43), residues: 312 helix: 4.34 (0.27), residues: 243 sheet: None (None), residues: 0 loop : -0.32 (0.70), residues: 69 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 31 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 34 average time/residue: 0.5785 time to fit residues: 20.8175 Evaluate side-chains 36 residues out of total 285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 31 time to evaluate : 0.283 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 3 average time/residue: 0.1657 time to fit residues: 0.9670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 0 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 11 optimal weight: 0.4980 chunk 29 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1173 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.150222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.135568 restraints weight = 3293.460| |-----------------------------------------------------------------------------| r_work (start): 0.4162 rms_B_bonded: 1.91 r_work: 0.4148 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.4134 rms_B_bonded: 1.70 restraints_weight: 0.2500 r_work: 0.4121 rms_B_bonded: 1.77 restraints_weight: 0.1250 r_work: 0.4106 rms_B_bonded: 1.89 restraints_weight: 0.0625 r_work: 0.4090 rms_B_bonded: 2.06 restraints_weight: 0.0312 r_work: 0.4072 rms_B_bonded: 2.28 restraints_weight: 0.0156 r_work: 0.4052 rms_B_bonded: 2.54 restraints_weight: 0.0078 r_work: 0.4030 rms_B_bonded: 2.85 restraints_weight: 0.0039 r_work: 0.4006 rms_B_bonded: 3.22 restraints_weight: 0.0020 r_work: 0.3978 rms_B_bonded: 3.65 restraints_weight: 0.0010 r_work: 0.3946 rms_B_bonded: 4.16 restraints_weight: 0.0005 r_work: 0.3910 rms_B_bonded: 4.75 restraints_weight: 0.0002 r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.027 2439 Z= 0.289 Angle : 0.476 8.090 3288 Z= 0.242 Chirality : 0.034 0.107 417 Planarity : 0.002 0.011 432 Dihedral : 3.224 9.398 324 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 1.75 % 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: 4.99 (0.44), residues: 312 helix: 4.15 (0.27), residues: 243 sheet: None (None), residues: 0 loop : -0.17 (0.75), residues: 69 =============================================================================== Job complete usr+sys time: 1066.76 seconds wall clock time: 20 minutes 33.71 seconds (1233.71 seconds total)