Starting phenix.real_space_refine (version: dev) on Tue Nov 29 11:49:43 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzs_24776/11_2022/7rzs_24776.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzs_24776/11_2022/7rzs_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_24776/11_2022/7rzs_24776.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzs_24776/11_2022/7rzs_24776.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzs_24776/11_2022/7rzs_24776.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzs_24776/11_2022/7rzs_24776.pdb" } resolution = 2.52 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= 0.019 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 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: 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: 1.71, per 1000 atoms: 0.70 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: 1.05 Conformation dependent library (CDL) restraints added in 364.5 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 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: 0.66 Time building geometry restraints manager: 1.13 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 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. 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: 0.640 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: 3.430 Check model and map are aligned: 0.040 Convert atoms to be neutral: 0.020 Process input model: 11.980 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:13.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 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 % 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 *********************** 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 : 0.285 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.5368 time to fit residues: 18.2874 Evaluate side-chains 32 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.282 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4076 ------------------------------------------------------------------------------- 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: 0.7853 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.028 2448 Z= 0.225 Angle : 0.373 4.027 3300 Z= 0.207 Chirality : 0.034 0.096 414 Planarity : 0.003 0.030 435 Dihedral : 3.304 11.742 324 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 0.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.15 (0.44), residues: 312 helix: 3.61 (0.27), residues: 246 sheet: None (None), residues: 0 loop : -0.99 (0.79), residues: 66 *********************** 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 : 0.321 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 29 average time/residue: 0.5290 time to fit residues: 16.3934 Evaluate side-chains 29 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.254 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3704 ------------------------------------------------------------------------------- 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: 0.9980 chunk 18 optimal weight: 0.6980 chunk 7 optimal weight: 0.2980 chunk 27 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 21 optimal weight: 5.9990 chunk 26 optimal weight: 0.4980 chunk 20 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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: 0.7849 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 2448 Z= 0.201 Angle : 0.339 5.809 3300 Z= 0.189 Chirality : 0.033 0.098 414 Planarity : 0.002 0.034 435 Dihedral : 3.057 10.213 324 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 0.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.22 (0.43), residues: 312 helix: 4.35 (0.26), residues: 246 sheet: None (None), residues: 0 loop : -0.53 (0.78), 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 31 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 29 time to evaluate : 0.396 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 29 average time/residue: 0.6314 time to fit residues: 19.3766 Evaluate side-chains 29 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.279 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4059 ------------------------------------------------------------------------------- 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: 0.9990 chunk 18 optimal weight: 0.5980 chunk 27 optimal weight: 0.0970 chunk 28 optimal weight: 0.7980 chunk 14 optimal weight: 0.0970 chunk 25 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 overall best weight: 0.4176 ------------------------------------------------------------------------------- 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: 0.7839 moved from start: 0.1696 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= 0.169 Angle : 0.326 6.256 3300 Z= 0.178 Chirality : 0.032 0.108 414 Planarity : 0.002 0.016 435 Dihedral : 2.891 9.550 324 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 0.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.70 (0.43), residues: 312 helix: 4.77 (0.26), residues: 243 sheet: None (None), residues: 0 loop : -0.45 (0.74), 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 29 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 27 time to evaluate : 0.427 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 28 average time/residue: 0.5648 time to fit residues: 17.0362 Evaluate side-chains 27 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.294 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4149 ------------------------------------------------------------------------------- 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: 0.0870 chunk 11 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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: 0.7852 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.016 2448 Z= 0.205 Angle : 0.334 6.623 3300 Z= 0.182 Chirality : 0.033 0.099 414 Planarity : 0.002 0.027 435 Dihedral : 2.927 10.021 324 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 0.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.75 (0.43), residues: 312 helix: 4.81 (0.26), residues: 243 sheet: None (None), residues: 0 loop : -0.46 (0.74), 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 30 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 28 time to evaluate : 0.281 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 28 average time/residue: 0.5237 time to fit residues: 15.6819 Evaluate side-chains 29 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 28 time to evaluate : 0.280 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 1.5632 time to fit residues: 1.9915 ------------------------------------------------------------------------------- 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: 1.9990 chunk 24 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 3 optimal weight: 0.4980 chunk 16 optimal weight: 0.2980 chunk 21 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.7859 moved from start: 0.1887 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= 0.231 Angle : 0.366 6.994 3300 Z= 0.197 Chirality : 0.034 0.133 414 Planarity : 0.001 0.008 435 Dihedral : 2.988 10.439 324 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 1.42 % 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: 4.64 (0.26), residues: 243 sheet: None (None), residues: 0 loop : -0.42 (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 31 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 27 time to evaluate : 0.316 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 30 average time/residue: 0.6015 time to fit residues: 19.0988 Evaluate side-chains 29 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 27 time to evaluate : 0.273 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.3965 ------------------------------------------------------------------------------- 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: 0.5980 chunk 24 optimal weight: 0.3980 chunk 28 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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: 0.7854 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.015 2448 Z= 0.211 Angle : 0.368 7.218 3300 Z= 0.195 Chirality : 0.034 0.171 414 Planarity : 0.001 0.011 435 Dihedral : 2.946 10.398 324 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 1.06 % 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: 5.56 (0.43), residues: 312 helix: 4.65 (0.26), residues: 243 sheet: None (None), residues: 0 loop : -0.40 (0.74), 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 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: symmetry clash outliers start: 3 outliers final: 2 residues processed: 30 average time/residue: 0.5003 time to fit residues: 16.0879 Evaluate side-chains 30 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 28 time to evaluate : 0.282 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.4086 ------------------------------------------------------------------------------- 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: 0.5980 chunk 22 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 27 optimal weight: 0.0570 chunk 25 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- 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: 0.7852 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.015 2448 Z= 0.203 Angle : 0.377 7.441 3300 Z= 0.196 Chirality : 0.035 0.194 414 Planarity : 0.002 0.020 435 Dihedral : 2.934 10.671 324 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 1.06 % 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 : -0.37 (0.74), 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 31 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 28 time to evaluate : 0.281 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 30 average time/residue: 0.5089 time to fit residues: 16.3315 Evaluate side-chains 30 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 28 time to evaluate : 0.274 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.3975 ------------------------------------------------------------------------------- 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: 1.9990 chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 14 optimal weight: 0.3980 chunk 25 optimal weight: 1.9990 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: 0.7862 moved from start: 0.2045 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= 0.244 Angle : 0.403 7.678 3300 Z= 0.207 Chirality : 0.036 0.231 414 Planarity : 0.002 0.010 435 Dihedral : 3.026 11.487 324 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 1.06 % 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: 5.50 (0.43), residues: 312 helix: 4.52 (0.26), residues: 246 sheet: None (None), residues: 0 loop : -0.28 (0.78), residues: 66 *********************** 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 31 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 28 time to evaluate : 0.302 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 30 average time/residue: 0.6481 time to fit residues: 20.7583 Evaluate side-chains 32 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 29 time to evaluate : 0.374 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 0.1208 time to fit residues: 0.6897 ------------------------------------------------------------------------------- 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: 0.0970 chunk 21 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 24 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 1 optimal weight: 0.0980 chunk 17 optimal weight: 0.5980 overall best weight: 0.4178 ------------------------------------------------------------------------------- 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: 0.7842 moved from start: 0.2040 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= 0.169 Angle : 0.384 7.674 3300 Z= 0.197 Chirality : 0.035 0.222 414 Planarity : 0.002 0.016 435 Dihedral : 2.922 12.410 324 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 1.06 % 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: 5.69 (0.43), residues: 312 helix: 4.73 (0.26), residues: 243 sheet: None (None), residues: 0 loop : -0.30 (0.76), 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 31 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 28 time to evaluate : 0.288 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 30 average time/residue: 0.5105 time to fit residues: 16.4524 Evaluate side-chains 30 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 28 time to evaluate : 0.364 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.4170 ------------------------------------------------------------------------------- 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: 0.0870 chunk 16 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 18 optimal weight: 0.4980 chunk 17 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 1 optimal weight: 0.0980 chunk 28 optimal weight: 3.9990 overall best weight: 0.3758 ------------------------------------------------------------------------------- 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 = 0.4275 r_free = 0.4275 target = 0.142508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.127840 restraints weight = 3178.464| |-----------------------------------------------------------------------------| r_work (start): 0.4057 rms_B_bonded: 2.22 r_work: 0.4043 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.4030 rms_B_bonded: 2.00 restraints_weight: 0.2500 r_work: 0.4017 rms_B_bonded: 2.04 restraints_weight: 0.1250 r_work: 0.4003 rms_B_bonded: 2.13 restraints_weight: 0.0625 r_work: 0.3988 rms_B_bonded: 2.26 restraints_weight: 0.0312 r_work: 0.3972 rms_B_bonded: 2.42 restraints_weight: 0.0156 r_work: 0.3955 rms_B_bonded: 2.62 restraints_weight: 0.0078 r_work: 0.3937 rms_B_bonded: 2.84 restraints_weight: 0.0039 r_work: 0.3917 rms_B_bonded: 3.10 restraints_weight: 0.0020 r_work: 0.3896 rms_B_bonded: 3.40 restraints_weight: 0.0010 r_work: 0.3872 rms_B_bonded: 3.74 restraints_weight: 0.0005 r_work: 0.3846 rms_B_bonded: 4.12 restraints_weight: 0.0002 r_work: 0.3818 rms_B_bonded: 4.55 restraints_weight: 0.0001 r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.014 2448 Z= 0.155 Angle : 0.394 7.621 3300 Z= 0.197 Chirality : 0.035 0.263 414 Planarity : 0.002 0.033 435 Dihedral : 2.873 12.429 324 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 0.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.82 (0.43), residues: 312 helix: 4.82 (0.26), residues: 243 sheet: None (None), residues: 0 loop : -0.25 (0.76), residues: 69 =============================================================================== Job complete usr+sys time: 981.83 seconds wall clock time: 18 minutes 45.93 seconds (1125.93 seconds total)