Starting phenix.real_space_refine (version: dev) on Thu May 12 15:43:51 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n7p_24230/05_2022/7n7p_24230_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n7p_24230/05_2022/7n7p_24230.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n7p_24230/05_2022/7n7p_24230.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n7p_24230/05_2022/7n7p_24230.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n7p_24230/05_2022/7n7p_24230_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n7p_24230/05_2022/7n7p_24230_neut_updated.pdb" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A GLU 28": "OE1" <-> "OE2" Residue "A GLU 60": "OE1" <-> "OE2" Residue "A PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 28": "OE1" <-> "OE2" Residue "B GLU 60": "OE1" <-> "OE2" Residue "B PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 5400 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2652 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 5, 'TRANS': 307} Chain breaks: 2 Chain: "B" Number of atoms: 2652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2652 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 5, 'TRANS': 307} Chain breaks: 2 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.54, per 1000 atoms: 0.66 Number of scatterers: 5400 At special positions: 0 Unit cell: (91.996, 91.996, 90.308, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 P 6 15.00 O 922 8.00 N 898 7.00 C 3542 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: 2.28 Conformation dependent library (CDL) restraints added in 684.5 milliseconds 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1192 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 18 helices and 0 sheets defined 85.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 9 through 68 removed outlier: 3.645A pdb=" N LYS A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 100 Processing helix chain 'A' and resid 107 through 112 Processing helix chain 'A' and resid 123 through 152 Processing helix chain 'A' and resid 158 through 185 Processing helix chain 'A' and resid 191 through 208 removed outlier: 3.836A pdb=" N PHE A 195 " --> pdb=" O GLY A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 253 removed outlier: 3.578A pdb=" N PHE A 219 " --> pdb=" O MET A 215 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ASN A 221 " --> pdb=" O GLN A 217 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N GLN A 222 " --> pdb=" O LYS A 218 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 236 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU A 253 " --> pdb=" O ARG A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 298 removed outlier: 3.591A pdb=" N SER A 266 " --> pdb=" O GLU A 262 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N TRP A 267 " --> pdb=" O GLY A 263 " (cutoff:3.500A) Proline residue: A 277 - end of helix removed outlier: 3.813A pdb=" N GLN A 298 " --> pdb=" O PHE A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 334 removed outlier: 3.614A pdb=" N PHE A 312 " --> pdb=" O LEU A 308 " (cutoff:3.500A) Proline residue: A 313 - end of helix Processing helix chain 'B' and resid 9 through 68 removed outlier: 3.645A pdb=" N LYS B 67 " --> pdb=" O LEU B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 100 Processing helix chain 'B' and resid 107 through 112 Processing helix chain 'B' and resid 123 through 152 Processing helix chain 'B' and resid 158 through 185 Processing helix chain 'B' and resid 191 through 208 removed outlier: 3.835A pdb=" N PHE B 195 " --> pdb=" O GLY B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 253 removed outlier: 3.578A pdb=" N PHE B 219 " --> pdb=" O MET B 215 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ASN B 221 " --> pdb=" O GLN B 217 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N GLN B 222 " --> pdb=" O LYS B 218 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU B 236 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU B 253 " --> pdb=" O ARG B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 298 removed outlier: 3.590A pdb=" N SER B 266 " --> pdb=" O GLU B 262 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N TRP B 267 " --> pdb=" O GLY B 263 " (cutoff:3.500A) Proline residue: B 277 - end of helix removed outlier: 3.813A pdb=" N GLN B 298 " --> pdb=" O PHE B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 334 removed outlier: 3.614A pdb=" N PHE B 312 " --> pdb=" O LEU B 308 " (cutoff:3.500A) Proline residue: B 313 - end of helix 430 hydrogen bonds defined for protein. 1290 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.46 Time building geometry restraints manager: 2.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.75: 5502 1.75 - 2.32: 46 2.32 - 2.89: 0 2.89 - 3.45: 2 3.45 - 4.02: 2 Bond restraints: 5552 Sorted by residual: bond pdb="AO6 COA A 401 " pdb="AP2 COA A 401 " ideal model delta sigma weight residual 1.610 4.022 -2.412 2.00e-02 2.50e+03 1.45e+04 bond pdb="AO6 COA B 401 " pdb="AP2 COA B 401 " ideal model delta sigma weight residual 1.610 4.022 -2.412 2.00e-02 2.50e+03 1.45e+04 bond pdb="AO5* COA A 401 " pdb="AP1 COA A 401 " ideal model delta sigma weight residual 1.610 3.428 -1.818 2.00e-02 2.50e+03 8.26e+03 bond pdb="AO5* COA B 401 " pdb="AP1 COA B 401 " ideal model delta sigma weight residual 1.610 3.428 -1.818 2.00e-02 2.50e+03 8.26e+03 bond pdb="PC9 COA B 401 " pdb="PO9 COA B 401 " ideal model delta sigma weight residual 1.410 1.185 0.225 2.00e-02 2.50e+03 1.27e+02 ... (remaining 5547 not shown) Histogram of bond angle deviations from ideal: 29.24 - 56.19: 4 56.19 - 83.14: 2 83.14 - 110.08: 843 110.08 - 137.03: 6649 137.03 - 163.98: 6 Bond angle restraints: 7504 Sorted by residual: angle pdb="AO3 COA A 401 " pdb="AP2 COA A 401 " pdb="AO6 COA A 401 " ideal model delta sigma weight residual 102.60 29.24 73.36 3.00e+00 1.11e-01 5.98e+02 angle pdb="AO3 COA B 401 " pdb="AP2 COA B 401 " pdb="AO6 COA B 401 " ideal model delta sigma weight residual 102.60 29.24 73.36 3.00e+00 1.11e-01 5.98e+02 angle pdb="AO3 COA A 401 " pdb="AP1 COA A 401 " pdb="AO5* COA A 401 " ideal model delta sigma weight residual 102.60 50.83 51.77 3.00e+00 1.11e-01 2.98e+02 angle pdb="AO3 COA B 401 " pdb="AP1 COA B 401 " pdb="AO5* COA B 401 " ideal model delta sigma weight residual 102.60 50.83 51.77 3.00e+00 1.11e-01 2.98e+02 angle pdb="AO2 COA B 401 " pdb="AP1 COA B 401 " pdb="AO5* COA B 401 " ideal model delta sigma weight residual 109.50 64.30 45.20 3.00e+00 1.11e-01 2.27e+02 ... (remaining 7499 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.15: 3074 35.15 - 70.31: 114 70.31 - 105.46: 8 105.46 - 140.62: 0 140.62 - 175.77: 6 Dihedral angle restraints: 3202 sinusoidal: 1360 harmonic: 1842 Sorted by residual: dihedral pdb="AC5* COA B 401 " pdb="AO5* COA B 401 " pdb="AP1 COA B 401 " pdb="AO3 COA B 401 " ideal model delta sinusoidal sigma weight residual -68.06 107.71 -175.77 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb="AC5* COA A 401 " pdb="AO5* COA A 401 " pdb="AP1 COA A 401 " pdb="AO3 COA A 401 " ideal model delta sinusoidal sigma weight residual -68.06 107.71 -175.77 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb="AO6 COA B 401 " pdb="PC11 COA B 401 " pdb="PC12 COA B 401 " pdb="PC10 COA B 401 " ideal model delta sinusoidal sigma weight residual 291.50 119.99 171.51 1 2.00e+01 2.50e-03 4.77e+01 ... (remaining 3199 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 531 0.031 - 0.062: 179 0.062 - 0.092: 50 0.092 - 0.123: 20 0.123 - 0.154: 8 Chirality restraints: 788 Sorted by residual: chirality pdb=" CB VAL A 118 " pdb=" CA VAL A 118 " pdb=" CG1 VAL A 118 " pdb=" CG2 VAL A 118 " both_signs ideal model delta sigma weight residual False -2.63 -2.78 0.15 2.00e-01 2.50e+01 5.90e-01 chirality pdb=" CB VAL B 118 " pdb=" CA VAL B 118 " pdb=" CG1 VAL B 118 " pdb=" CG2 VAL B 118 " both_signs ideal model delta sigma weight residual False -2.63 -2.78 0.15 2.00e-01 2.50e+01 5.90e-01 chirality pdb=" CA PRO B 313 " pdb=" N PRO B 313 " pdb=" C PRO B 313 " pdb=" CB PRO B 313 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.76e-01 ... (remaining 785 not shown) Planarity restraints: 914 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 198 " -0.015 2.00e-02 2.50e+03 1.61e-02 5.18e+00 pdb=" CG TYR A 198 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR A 198 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR A 198 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR A 198 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 198 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 198 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 198 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 198 " 0.015 2.00e-02 2.50e+03 1.59e-02 5.08e+00 pdb=" CG TYR B 198 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR B 198 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR B 198 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR B 198 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 198 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR B 198 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 198 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 23 " -0.016 2.00e-02 2.50e+03 1.50e-02 3.91e+00 pdb=" CG PHE B 23 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE B 23 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE B 23 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE B 23 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 23 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE B 23 " -0.000 2.00e-02 2.50e+03 ... (remaining 911 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.30: 4 2.30 - 2.95: 2112 2.95 - 3.60: 8699 3.60 - 4.25: 12242 4.25 - 4.90: 21030 Nonbonded interactions: 44087 Sorted by model distance: nonbonded pdb="AO6 COA A 401 " pdb="AP1 COA A 401 " model vdw 1.647 2.720 nonbonded pdb="AO6 COA B 401 " pdb="AP1 COA B 401 " model vdw 1.647 2.720 nonbonded pdb="AO5* COA B 401 " pdb="AP2 COA B 401 " model vdw 1.647 2.720 nonbonded pdb="AO5* COA A 401 " pdb="AP2 COA A 401 " model vdw 1.647 2.720 nonbonded pdb=" O LEU A 120 " pdb=" NZ LYS A 126 " model vdw 2.364 2.520 ... (remaining 44082 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 32 5.16 5 C 3542 2.51 5 N 898 2.21 5 O 922 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: 0.870 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: 0.010 Extract box with map and model: 5.440 Check model and map are aligned: 0.080 Convert atoms to be neutral: 0.050 Process input model: 18.290 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 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 : 0.058 2.412 5552 Z= 4.279 Angle : 2.032 73.355 7504 Z= 0.727 Chirality : 0.038 0.154 788 Planarity : 0.004 0.039 914 Dihedral : 19.969 175.773 2010 Min Nonbonded Distance : 1.647 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer Outliers : 0.35 % 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: 1.62 (0.29), residues: 614 helix: 1.66 (0.19), residues: 526 sheet: None (None), residues: 0 loop : -2.52 (0.51), residues: 88 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 90 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 88 time to evaluate : 0.694 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 88 average time/residue: 0.2203 time to fit residues: 24.1729 Evaluate side-chains 76 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.661 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 chunk 25 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 56 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN B 45 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 5552 Z= 0.180 Angle : 0.550 7.569 7504 Z= 0.253 Chirality : 0.033 0.161 788 Planarity : 0.003 0.028 914 Dihedral : 13.032 126.818 728 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer Outliers : 1.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.76 (0.30), residues: 614 helix: 2.44 (0.19), residues: 528 sheet: None (None), residues: 0 loop : -2.35 (0.52), residues: 86 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 88 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 82 time to evaluate : 0.639 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 86 average time/residue: 0.1731 time to fit residues: 19.6217 Evaluate side-chains 74 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 68 time to evaluate : 0.637 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0528 time to fit residues: 1.4547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 50 optimal weight: 0.3980 chunk 55 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN B 45 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 5552 Z= 0.166 Angle : 0.512 7.092 7504 Z= 0.239 Chirality : 0.033 0.187 788 Planarity : 0.003 0.025 914 Dihedral : 10.061 102.403 728 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer Outliers : 0.17 % 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: 3.24 (0.30), residues: 614 helix: 2.77 (0.19), residues: 528 sheet: None (None), residues: 0 loop : -2.26 (0.53), residues: 86 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 93 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 92 time to evaluate : 0.628 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 92 average time/residue: 0.2032 time to fit residues: 23.7278 Evaluate side-chains 75 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.578 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN B 45 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 5552 Z= 0.187 Angle : 0.535 7.787 7504 Z= 0.249 Chirality : 0.033 0.187 788 Planarity : 0.003 0.024 914 Dihedral : 9.433 98.577 728 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer Outliers : 0.87 % 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: 3.35 (0.31), residues: 614 helix: 2.85 (0.19), residues: 528 sheet: None (None), residues: 0 loop : -2.27 (0.54), residues: 86 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 93 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 88 time to evaluate : 0.710 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 90 average time/residue: 0.1890 time to fit residues: 21.9060 Evaluate side-chains 84 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 80 time to evaluate : 0.649 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0584 time to fit residues: 1.2874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 51 optimal weight: 0.5980 chunk 41 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN A 54 GLN B 45 ASN B 54 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 5552 Z= 0.210 Angle : 0.539 7.236 7504 Z= 0.253 Chirality : 0.034 0.193 788 Planarity : 0.003 0.024 914 Dihedral : 8.962 93.991 728 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer Outliers : 0.52 % 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: 3.35 (0.31), residues: 614 helix: 2.85 (0.20), residues: 528 sheet: None (None), residues: 0 loop : -2.22 (0.55), residues: 86 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 87 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 84 time to evaluate : 0.685 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 86 average time/residue: 0.2079 time to fit residues: 22.6504 Evaluate side-chains 78 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.636 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 31 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN A 54 GLN B 45 ASN B 54 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 5552 Z= 0.186 Angle : 0.538 8.505 7504 Z= 0.252 Chirality : 0.033 0.186 788 Planarity : 0.003 0.024 914 Dihedral : 8.655 90.038 728 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.43 (0.31), residues: 614 helix: 2.90 (0.20), residues: 528 sheet: None (None), residues: 0 loop : -2.21 (0.54), residues: 86 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 89 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 85 time to evaluate : 0.616 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 89 average time/residue: 0.2031 time to fit residues: 23.0374 Evaluate side-chains 82 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 80 time to evaluate : 0.689 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0540 time to fit residues: 1.1406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 23 optimal weight: 8.9990 chunk 35 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 5552 Z= 0.209 Angle : 0.578 8.599 7504 Z= 0.266 Chirality : 0.034 0.176 788 Planarity : 0.003 0.052 914 Dihedral : 8.566 87.539 728 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer Outliers : 1.05 % 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: 3.46 (0.31), residues: 614 helix: 2.89 (0.20), residues: 528 sheet: None (None), residues: 0 loop : -1.99 (0.58), residues: 86 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 93 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 87 time to evaluate : 0.668 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 89 average time/residue: 0.2241 time to fit residues: 24.8837 Evaluate side-chains 85 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 82 time to evaluate : 0.664 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0542 time to fit residues: 1.2144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 54 optimal weight: 8.9990 chunk 57 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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: 0.8395 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 5552 Z= 0.194 Angle : 0.565 9.649 7504 Z= 0.262 Chirality : 0.033 0.173 788 Planarity : 0.003 0.027 914 Dihedral : 8.398 84.441 728 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.50 (0.31), residues: 614 helix: 2.92 (0.20), residues: 528 sheet: None (None), residues: 0 loop : -1.96 (0.58), residues: 86 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 90 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 86 time to evaluate : 0.667 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 88 average time/residue: 0.2117 time to fit residues: 23.5260 Evaluate side-chains 84 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 82 time to evaluate : 0.658 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0530 time to fit residues: 1.0852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 17 optimal weight: 0.0970 chunk 50 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 58 optimal weight: 0.3980 chunk 35 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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: 0.8365 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 5552 Z= 0.160 Angle : 0.548 10.056 7504 Z= 0.255 Chirality : 0.033 0.166 788 Planarity : 0.003 0.024 914 Dihedral : 8.092 77.956 728 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % 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: 3.55 (0.31), residues: 614 helix: 2.96 (0.20), residues: 530 sheet: None (None), residues: 0 loop : -2.15 (0.56), residues: 84 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 90 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.633 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.2168 time to fit residues: 24.5623 Evaluate side-chains 84 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.695 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 39 optimal weight: 0.0070 chunk 52 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 overall best weight: 0.5598 ------------------------------------------------------------------------------- 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: 0.8353 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 5552 Z= 0.159 Angle : 0.551 10.408 7504 Z= 0.258 Chirality : 0.033 0.152 788 Planarity : 0.003 0.028 914 Dihedral : 7.880 72.891 728 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % 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: 3.66 (0.31), residues: 614 helix: 3.04 (0.20), residues: 530 sheet: None (None), residues: 0 loop : -2.20 (0.55), residues: 84 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 87 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.600 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.2024 time to fit residues: 22.5551 Evaluate side-chains 83 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.643 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 56 optimal weight: 0.4980 chunk 33 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 GLN ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.162332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.118422 restraints weight = 6242.349| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.67 r_work: 0.3316 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 1.55 restraints_weight: 0.2500 r_work: 0.3266 rms_B_bonded: 1.74 restraints_weight: 0.1250 r_work: 0.3235 rms_B_bonded: 2.05 restraints_weight: 0.0625 r_work: 0.3195 rms_B_bonded: 2.52 restraints_weight: 0.0312 r_work: 0.3145 rms_B_bonded: 3.20 restraints_weight: 0.0156 r_work: 0.3077 rms_B_bonded: 4.18 restraints_weight: 0.0078 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 5552 Z= 0.183 Angle : 0.559 10.313 7504 Z= 0.266 Chirality : 0.033 0.151 788 Planarity : 0.004 0.055 914 Dihedral : 7.870 71.867 728 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % 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: 3.61 (0.31), residues: 614 helix: 3.01 (0.20), residues: 528 sheet: None (None), residues: 0 loop : -2.01 (0.56), residues: 86 =============================================================================== Job complete usr+sys time: 1273.07 seconds wall clock time: 23 minutes 49.21 seconds (1429.21 seconds total)