Starting phenix.real_space_refine on Sun Mar 10 14:52:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzs_24776/03_2024/7rzs_24776.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzs_24776/03_2024/7rzs_24776.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzs_24776/03_2024/7rzs_24776.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzs_24776/03_2024/7rzs_24776.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzs_24776/03_2024/7rzs_24776.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzs_24776/03_2024/7rzs_24776.pdb" } resolution = 2.52 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 1509 2.51 5 N 426 2.21 5 O 510 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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-5265/modules/chem_data/mon_lib" Total number of atoms: 2445 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 534 Classifications: {'peptide': 71} Link IDs: {'TRANS': 70} Chain: "B" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 534 Classifications: {'peptide': 71} Link IDs: {'TRANS': 70} Chain: "C" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 534 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: 1.63, per 1000 atoms: 0.67 Number of scatterers: 2445 At special positions: 0 Unit cell: (50.6075, 42.445, 115.908, 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 510 8.00 N 426 7.00 C 1509 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: 0.94 Conformation dependent library (CDL) restraints added in 422.6 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: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 918 through 988 Processing helix chain 'B' and resid 919 through 988 Processing helix chain 'C' and resid 919 through 988 Processing helix chain 'D' and resid 1179 through 1193 Processing helix chain 'D' and resid 1194 through 1197 removed outlier: 3.569A 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: 3.569A 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: 3.570A pdb=" N LEU F1197 " --> pdb=" O ASN F1194 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 1194 through 1197' 232 hydrogen bonds defined for protein. 696 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: 0.68 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 465 1.29 - 1.35: 399 1.35 - 1.41: 63 1.41 - 1.48: 366 1.48 - 1.54: 1155 Bond restraints: 2448 Sorted by residual: 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 6.83e-01 bond pdb=" C ILE F1179 " pdb=" O ILE F1179 " ideal model delta sigma weight residual 1.236 1.227 0.009 1.19e-02 7.06e+03 6.37e-01 bond pdb=" C ILE D1179 " pdb=" O ILE D1179 " ideal model delta sigma weight residual 1.236 1.227 0.009 1.19e-02 7.06e+03 6.34e-01 bond pdb=" N VAL E1176 " pdb=" CA VAL E1176 " ideal model delta sigma weight residual 1.457 1.448 0.009 1.15e-02 7.56e+03 5.87e-01 bond pdb=" N ILE E1179 " pdb=" CA ILE E1179 " ideal model delta sigma weight residual 1.459 1.450 0.009 1.25e-02 6.40e+03 5.42e-01 ... (remaining 2443 not shown) Histogram of bond angle deviations from ideal: 106.69 - 110.25: 351 110.25 - 113.80: 1162 113.80 - 117.36: 323 117.36 - 120.91: 924 120.91 - 124.47: 540 Bond angle restraints: 3300 Sorted by residual: angle pdb=" CA ARG B 983 " pdb=" CB ARG B 983 " pdb=" CG ARG B 983 " ideal model delta sigma weight residual 114.10 118.77 -4.67 2.00e+00 2.50e-01 5.46e+00 angle pdb=" CA ARG A 983 " pdb=" CB ARG A 983 " pdb=" CG ARG A 983 " ideal model delta sigma weight residual 114.10 118.77 -4.67 2.00e+00 2.50e-01 5.44e+00 angle pdb=" CA ARG C 983 " pdb=" CB ARG C 983 " pdb=" CG ARG C 983 " ideal model delta sigma weight residual 114.10 118.72 -4.62 2.00e+00 2.50e-01 5.34e+00 angle pdb=" C ARG C 983 " pdb=" CA ARG C 983 " pdb=" CB ARG C 983 " ideal model delta sigma weight residual 110.31 113.88 -3.57 2.09e+00 2.29e-01 2.92e+00 angle pdb=" C ARG B 983 " pdb=" CA ARG B 983 " pdb=" CB ARG B 983 " ideal model delta sigma weight residual 110.31 113.86 -3.55 2.09e+00 2.29e-01 2.89e+00 ... (remaining 3295 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 1389 17.76 - 35.52: 111 35.52 - 53.28: 12 53.28 - 71.05: 9 71.05 - 88.81: 6 Dihedral angle restraints: 1527 sinusoidal: 591 harmonic: 936 Sorted by residual: dihedral pdb=" CG ARG A 983 " pdb=" CD ARG A 983 " pdb=" NE ARG A 983 " pdb=" CZ ARG A 983 " ideal model delta sinusoidal sigma weight residual -90.00 -130.02 40.02 2 1.50e+01 4.44e-03 8.82e+00 dihedral pdb=" CG ARG C 983 " pdb=" CD ARG C 983 " pdb=" NE ARG C 983 " pdb=" CZ ARG C 983 " ideal model delta sinusoidal sigma weight residual -90.00 -130.01 40.01 2 1.50e+01 4.44e-03 8.82e+00 dihedral pdb=" CG ARG B 983 " pdb=" CD ARG B 983 " pdb=" NE ARG B 983 " pdb=" CZ ARG B 983 " ideal model delta sinusoidal sigma weight residual -90.00 -130.01 40.01 2 1.50e+01 4.44e-03 8.82e+00 ... (remaining 1524 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 212 0.023 - 0.046: 134 0.046 - 0.068: 53 0.068 - 0.091: 7 0.091 - 0.114: 8 Chirality restraints: 414 Sorted by residual: chirality pdb=" CA PHE C 970 " pdb=" N PHE C 970 " pdb=" C PHE C 970 " pdb=" CB PHE C 970 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 3.24e-01 chirality pdb=" CA PHE A 970 " pdb=" N PHE A 970 " pdb=" C PHE A 970 " pdb=" CB PHE A 970 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 3.15e-01 chirality pdb=" CA PHE B 970 " pdb=" N PHE B 970 " pdb=" C PHE B 970 " pdb=" CB PHE B 970 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 3.10e-01 ... (remaining 411 not shown) Planarity restraints: 435 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 983 " 0.007 2.00e-02 2.50e+03 1.44e-02 2.08e+00 pdb=" C ARG A 983 " -0.025 2.00e-02 2.50e+03 pdb=" O ARG A 983 " 0.009 2.00e-02 2.50e+03 pdb=" N LEU A 984 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 983 " -0.007 2.00e-02 2.50e+03 1.42e-02 2.01e+00 pdb=" C ARG C 983 " 0.024 2.00e-02 2.50e+03 pdb=" O ARG C 983 " -0.009 2.00e-02 2.50e+03 pdb=" N LEU C 984 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 983 " -0.007 2.00e-02 2.50e+03 1.41e-02 2.00e+00 pdb=" C ARG B 983 " 0.024 2.00e-02 2.50e+03 pdb=" O ARG B 983 " -0.009 2.00e-02 2.50e+03 pdb=" N LEU B 984 " -0.008 2.00e-02 2.50e+03 ... (remaining 432 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 600 2.80 - 3.32: 2636 3.32 - 3.85: 4135 3.85 - 4.37: 4614 4.37 - 4.90: 8090 Nonbonded interactions: 20075 Sorted by model distance: nonbonded pdb=" O GLY B 971 " pdb=" OG SER B 974 " model vdw 2.273 2.440 nonbonded pdb=" O GLY A 971 " pdb=" OG SER A 974 " model vdw 2.273 2.440 nonbonded pdb=" O GLY C 971 " pdb=" OG SER C 974 " model vdw 2.273 2.440 nonbonded pdb=" NE2 GLN B 935 " pdb=" O ALA E1190 " model vdw 2.506 2.520 nonbonded pdb=" NE2 GLN A 935 " pdb=" O ALA D1190 " model vdw 2.507 2.520 ... (remaining 20070 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 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: 0.870 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: 3.360 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.770 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.022 2448 Z= 0.315 Angle : 0.461 4.674 3300 Z= 0.271 Chirality : 0.034 0.114 414 Planarity : 0.004 0.041 435 Dihedral : 14.727 88.807 909 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.98 (0.43), residues: 312 helix: 2.03 (0.27), residues: 246 sheet: None (None), residues: 0 loop : -1.53 (0.82), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.003 PHE B 970 ARG 0.011 0.003 ARG B 983 *********************** 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 32 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: A 980 ILE cc_start: 0.8695 (mt) cc_final: 0.8461 (mt) REVERT: C 965 GLN cc_start: 0.8146 (mm110) cc_final: 0.7903 (mm110) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.5929 time to fit residues: 20.1200 Evaluate side-chains 32 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.280 ------------------------------------------------------------------------------- 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: 0.9990 chunk 22 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 7 optimal weight: 0.4980 chunk 15 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 978 ASN C 978 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2448 Z= 0.226 Angle : 0.369 4.041 3300 Z= 0.206 Chirality : 0.033 0.095 414 Planarity : 0.002 0.027 435 Dihedral : 3.313 11.726 324 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.71 % Allowed : 7.80 % Favored : 91.49 % 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: 4.14 (0.44), residues: 312 helix: 3.60 (0.27), residues: 246 sheet: None (None), residues: 0 loop : -1.00 (0.79), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.002 PHE C 970 ARG 0.007 0.001 ARG A 983 *********************** 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 31 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 29 time to evaluate : 0.268 Fit side-chains REVERT: C 965 GLN cc_start: 0.8142 (mm110) cc_final: 0.7901 (mm110) outliers start: 2 outliers final: 0 residues processed: 29 average time/residue: 0.5586 time to fit residues: 17.1676 Evaluate side-chains 29 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.228 ------------------------------------------------------------------------------- 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: 0.7980 chunk 18 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 24 optimal weight: 0.0570 chunk 9 optimal weight: 0.5980 chunk 21 optimal weight: 6.9990 chunk 26 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- 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: 0.7474 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2448 Z= 0.192 Angle : 0.338 5.830 3300 Z= 0.188 Chirality : 0.033 0.098 414 Planarity : 0.002 0.034 435 Dihedral : 3.050 10.181 324 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.71 % Allowed : 8.87 % Favored : 90.43 % 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: 5.25 (0.43), residues: 312 helix: 4.37 (0.26), residues: 246 sheet: None (None), residues: 0 loop : -0.53 (0.78), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE A 970 ARG 0.005 0.001 ARG A 983 *********************** 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 30 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 28 time to evaluate : 0.222 Fit side-chains REVERT: C 965 GLN cc_start: 0.8145 (mm110) cc_final: 0.7897 (mm110) outliers start: 2 outliers final: 0 residues processed: 28 average time/residue: 0.4535 time to fit residues: 13.4949 Evaluate side-chains 28 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.200 ------------------------------------------------------------------------------- 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: 0.0670 chunk 18 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 14 optimal weight: 0.0970 chunk 25 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 overall best weight: 0.3916 ------------------------------------------------------------------------------- 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: 0.7458 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2448 Z= 0.161 Angle : 0.325 6.223 3300 Z= 0.178 Chirality : 0.032 0.108 414 Planarity : 0.002 0.012 435 Dihedral : 2.922 9.569 324 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.35 % Allowed : 10.64 % Favored : 89.01 % 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: 5.64 (0.43), residues: 312 helix: 4.72 (0.26), residues: 243 sheet: None (None), residues: 0 loop : -0.44 (0.75), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.001 PHE B 970 ARG 0.003 0.001 ARG A 983 *********************** 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 29 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 28 time to evaluate : 0.287 Fit side-chains REVERT: C 965 GLN cc_start: 0.8142 (mm110) cc_final: 0.7894 (mm110) outliers start: 1 outliers final: 0 residues processed: 28 average time/residue: 0.5667 time to fit residues: 16.9121 Evaluate side-chains 28 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.274 ------------------------------------------------------------------------------- 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: 0.0970 chunk 11 optimal weight: 0.5980 chunk 24 optimal weight: 0.0670 chunk 20 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 9 optimal weight: 0.3980 chunk 5 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 overall best weight: 0.3516 ------------------------------------------------------------------------------- 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: 0.7456 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 2448 Z= 0.146 Angle : 0.329 6.450 3300 Z= 0.177 Chirality : 0.033 0.112 414 Planarity : 0.002 0.014 435 Dihedral : 2.818 9.480 324 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.42 % Allowed : 8.87 % Favored : 89.72 % 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: 5.91 (0.43), residues: 312 helix: 4.92 (0.25), residues: 243 sheet: None (None), residues: 0 loop : -0.40 (0.73), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.001 PHE B 938 ARG 0.003 0.001 ARG C 983 *********************** 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 30 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 26 time to evaluate : 0.281 Fit side-chains REVERT: C 965 GLN cc_start: 0.8143 (mm110) cc_final: 0.7888 (mm110) REVERT: C 970 PHE cc_start: 0.7961 (OUTLIER) cc_final: 0.7727 (m-10) outliers start: 4 outliers final: 0 residues processed: 28 average time/residue: 0.5829 time to fit residues: 17.3491 Evaluate side-chains 27 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 26 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 970 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 24 optimal weight: 0.0670 chunk 13 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 21 optimal weight: 4.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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: 0.7482 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2448 Z= 0.223 Angle : 0.361 6.815 3300 Z= 0.193 Chirality : 0.034 0.155 414 Planarity : 0.002 0.011 435 Dihedral : 2.962 10.132 324 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.06 % Allowed : 9.57 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.62 (0.43), residues: 312 helix: 4.70 (0.26), residues: 243 sheet: None (None), residues: 0 loop : -0.40 (0.74), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.002 PHE B 970 ARG 0.004 0.001 ARG C 983 *********************** 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 31 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 28 time to evaluate : 0.277 Fit side-chains REVERT: C 965 GLN cc_start: 0.8136 (mm110) cc_final: 0.7890 (mm110) REVERT: C 970 PHE cc_start: 0.8015 (OUTLIER) cc_final: 0.7775 (m-10) outliers start: 3 outliers final: 0 residues processed: 29 average time/residue: 0.5761 time to fit residues: 17.7381 Evaluate side-chains 29 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 28 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 970 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.7487 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.017 2448 Z= 0.243 Angle : 0.389 7.148 3300 Z= 0.205 Chirality : 0.036 0.213 414 Planarity : 0.002 0.008 435 Dihedral : 2.996 10.224 324 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.42 % Allowed : 9.57 % Favored : 89.01 % 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: 5.43 (0.43), residues: 312 helix: 4.54 (0.26), residues: 243 sheet: None (None), residues: 0 loop : -0.40 (0.74), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.002 PHE B 938 ARG 0.004 0.001 ARG C 983 *********************** 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 33 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 29 time to evaluate : 0.279 Fit side-chains REVERT: C 965 GLN cc_start: 0.8132 (mm110) cc_final: 0.7886 (mm110) REVERT: C 970 PHE cc_start: 0.8013 (OUTLIER) cc_final: 0.7774 (m-10) outliers start: 4 outliers final: 2 residues processed: 31 average time/residue: 0.6461 time to fit residues: 21.1119 Evaluate side-chains 32 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 29 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain C residue 970 PHE Chi-restraints excluded: chain C residue 981 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.7492 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 2448 Z= 0.250 Angle : 0.405 8.584 3300 Z= 0.209 Chirality : 0.036 0.198 414 Planarity : 0.002 0.014 435 Dihedral : 3.030 10.749 324 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.42 % Allowed : 9.22 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.48 (0.43), residues: 312 helix: 4.52 (0.26), residues: 246 sheet: None (None), residues: 0 loop : -0.35 (0.77), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.002 PHE B 938 ARG 0.006 0.001 ARG C 983 *********************** 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 32 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 28 time to evaluate : 0.248 Fit side-chains revert: symmetry clash REVERT: C 965 GLN cc_start: 0.8134 (mm110) cc_final: 0.7886 (mm110) REVERT: C 970 PHE cc_start: 0.8016 (OUTLIER) cc_final: 0.7802 (m-10) outliers start: 4 outliers final: 3 residues processed: 31 average time/residue: 0.6708 time to fit residues: 21.8381 Evaluate side-chains 32 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 28 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain C residue 970 PHE Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 984 LEU 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: 0.6980 chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.7496 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 2448 Z= 0.270 Angle : 0.409 7.541 3300 Z= 0.213 Chirality : 0.036 0.196 414 Planarity : 0.002 0.021 435 Dihedral : 3.077 11.300 324 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.42 % Allowed : 9.57 % Favored : 89.01 % 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: 4.42 (0.26), residues: 246 sheet: None (None), residues: 0 loop : -0.30 (0.78), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.002 PHE B 938 ARG 0.006 0.001 ARG C 983 *********************** 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 33 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 29 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: C 965 GLN cc_start: 0.8137 (mm110) cc_final: 0.7899 (mm110) REVERT: C 970 PHE cc_start: 0.8052 (OUTLIER) cc_final: 0.7839 (m-10) outliers start: 4 outliers final: 3 residues processed: 32 average time/residue: 0.6416 time to fit residues: 21.5968 Evaluate side-chains 33 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 29 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain C residue 970 PHE Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 984 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 0.0470 chunk 21 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 overall best weight: 0.4878 ------------------------------------------------------------------------------- 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: 0.7476 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 2448 Z= 0.190 Angle : 0.397 7.346 3300 Z= 0.204 Chirality : 0.035 0.196 414 Planarity : 0.002 0.023 435 Dihedral : 2.975 11.371 324 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.42 % Allowed : 9.57 % Favored : 89.01 % 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: 5.54 (0.43), residues: 312 helix: 4.61 (0.26), residues: 243 sheet: None (None), residues: 0 loop : -0.30 (0.75), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.001 PHE B 938 ARG 0.006 0.001 ARG C 983 ********************** 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 32 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 28 time to evaluate : 0.275 Fit side-chains revert: symmetry clash REVERT: C 965 GLN cc_start: 0.8132 (mm110) cc_final: 0.7886 (mm110) REVERT: C 970 PHE cc_start: 0.8009 (OUTLIER) cc_final: 0.7783 (m-10) outliers start: 4 outliers final: 2 residues processed: 31 average time/residue: 0.5310 time to fit residues: 17.5510 Evaluate side-chains 31 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 28 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain C residue 970 PHE Chi-restraints excluded: chain C residue 984 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 0.3980 chunk 16 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 11 optimal weight: 0.2980 chunk 29 optimal weight: 0.7980 chunk 1 optimal weight: 0.3980 chunk 28 optimal weight: 3.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.141604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.127028 restraints weight = 3162.888| |-----------------------------------------------------------------------------| r_work (start): 0.4047 rms_B_bonded: 2.18 r_work: 0.3899 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3721 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.013 2448 Z= 0.181 Angle : 0.383 7.537 3300 Z= 0.198 Chirality : 0.035 0.199 414 Planarity : 0.002 0.020 435 Dihedral : 2.930 11.586 324 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.42 % Allowed : 9.57 % Favored : 89.01 % 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: 5.62 (0.43), residues: 312 helix: 4.66 (0.26), residues: 243 sheet: None (None), residues: 0 loop : -0.27 (0.76), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.001 PHE C 970 ARG 0.005 0.001 ARG A 983 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1091.02 seconds wall clock time: 20 minutes 18.85 seconds (1218.85 seconds total)