Starting phenix.real_space_refine on Tue Feb 13 10:29:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n7p_24230/02_2024/7n7p_24230_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n7p_24230/02_2024/7n7p_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_24230/02_2024/7n7p_24230.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n7p_24230/02_2024/7n7p_24230.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n7p_24230/02_2024/7n7p_24230_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n7p_24230/02_2024/7n7p_24230_neut_updated.pdb" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 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. 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-5238/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: 3.36, per 1000 atoms: 0.62 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: 2.16 Conformation dependent library (CDL) restraints added in 894.9 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: 0.83 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: 1.38 Time building geometry restraints manager: 2.27 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=" AP1 COA A 401 " pdb="AO5* 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=" AP1 COA B 401 " pdb="AO5* 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=" AO3 COA B 401 " pdb=" AP1 COA B 401 " pdb="AO5* COA B 401 " pdb="AC5* 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=" AO3 COA A 401 " pdb=" AP1 COA A 401 " pdb="AO5* COA A 401 " pdb="AC5* 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=" AP2 COA B 401 " pdb="AO5* COA B 401 " model vdw 1.647 2.720 nonbonded pdb=" AP2 COA A 401 " pdb="AO5* 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 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: 1.880 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: 5.380 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 18.430 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 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= 3.088 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 : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.35 % Allowed : 1.05 % Favored : 98.61 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 267 HIS 0.002 0.001 HIS B 30 PHE 0.034 0.002 PHE B 23 TYR 0.040 0.002 TYR A 198 ARG 0.009 0.001 ARG B 57 *********************** 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 : 0.641 Fit side-chains REVERT: A 45 ASN cc_start: 0.8018 (m110) cc_final: 0.7441 (m110) REVERT: A 56 LYS cc_start: 0.8143 (tppt) cc_final: 0.7817 (tppp) REVERT: B 45 ASN cc_start: 0.8021 (m110) cc_final: 0.7445 (m110) REVERT: B 56 LYS cc_start: 0.8143 (tppt) cc_final: 0.7801 (tppp) outliers start: 2 outliers final: 0 residues processed: 88 average time/residue: 0.2364 time to fit residues: 25.7429 Evaluate side-chains 78 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.602 ------------------------------------------------------------------------------- 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: 0.6980 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: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 GLN ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 241 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.0985 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= 0.179 Angle : 0.556 8.066 7504 Z= 0.255 Chirality : 0.032 0.135 788 Planarity : 0.003 0.028 914 Dihedral : 12.920 124.516 728 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.05 % Allowed : 8.19 % Favored : 90.77 % 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: 2.80 (0.30), residues: 614 helix: 2.47 (0.19), residues: 528 sheet: None (None), residues: 0 loop : -2.35 (0.52), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 192 HIS 0.001 0.000 HIS B 30 PHE 0.029 0.001 PHE A 23 TYR 0.018 0.002 TYR B 198 ARG 0.003 0.000 ARG B 57 *********************** 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 90 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 84 time to evaluate : 0.573 Fit side-chains REVERT: A 45 ASN cc_start: 0.7997 (m110) cc_final: 0.7427 (m110) REVERT: B 45 ASN cc_start: 0.8003 (m110) cc_final: 0.7430 (m110) outliers start: 6 outliers final: 6 residues processed: 88 average time/residue: 0.1774 time to fit residues: 20.4428 Evaluate side-chains 76 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 70 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain B residue 46 ASN Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 307 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 0.3980 chunk 17 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 19 optimal weight: 0.0980 chunk 45 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 GLN ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 241 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5552 Z= 0.153 Angle : 0.502 7.264 7504 Z= 0.233 Chirality : 0.032 0.189 788 Planarity : 0.003 0.025 914 Dihedral : 10.041 103.037 728 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.22 % Allowed : 9.41 % Favored : 89.37 % 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: 3.40 (0.30), residues: 614 helix: 2.88 (0.19), residues: 528 sheet: None (None), residues: 0 loop : -2.24 (0.53), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 267 HIS 0.002 0.001 HIS B 283 PHE 0.021 0.001 PHE B 23 TYR 0.015 0.001 TYR A 198 ARG 0.005 0.000 ARG B 57 *********************** 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 100 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 93 time to evaluate : 0.625 Fit side-chains REVERT: A 198 TYR cc_start: 0.8919 (m-80) cc_final: 0.8682 (m-80) REVERT: B 198 TYR cc_start: 0.8924 (m-80) cc_final: 0.8684 (m-80) outliers start: 7 outliers final: 6 residues processed: 97 average time/residue: 0.2162 time to fit residues: 26.1908 Evaluate side-chains 87 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 81 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain B residue 46 ASN Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 307 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 6 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 59 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 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 54 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1339 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 : 0.517 7.521 7504 Z= 0.240 Chirality : 0.033 0.186 788 Planarity : 0.003 0.025 914 Dihedral : 9.331 97.911 728 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.74 % Allowed : 10.28 % Favored : 87.98 % 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: 3.56 (0.31), residues: 614 helix: 3.00 (0.19), residues: 528 sheet: None (None), residues: 0 loop : -2.25 (0.54), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 267 HIS 0.003 0.001 HIS B 283 PHE 0.022 0.001 PHE B 23 TYR 0.012 0.001 TYR B 133 ARG 0.004 0.000 ARG B 57 *********************** 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 102 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 92 time to evaluate : 0.634 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 99 average time/residue: 0.2010 time to fit residues: 25.2095 Evaluate side-chains 92 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 84 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 94 PHE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain B residue 46 ASN Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 307 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 44 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 51 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1503 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= 0.178 Angle : 0.516 8.131 7504 Z= 0.241 Chirality : 0.033 0.188 788 Planarity : 0.003 0.025 914 Dihedral : 8.867 93.168 728 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.57 % Allowed : 12.02 % Favored : 86.41 % 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: 3.59 (0.31), residues: 614 helix: 3.02 (0.19), residues: 528 sheet: None (None), residues: 0 loop : -2.23 (0.54), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 192 HIS 0.004 0.001 HIS B 283 PHE 0.023 0.001 PHE A 23 TYR 0.014 0.002 TYR A 198 ARG 0.004 0.000 ARG B 57 *********************** 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 93 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 84 time to evaluate : 0.606 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 91 average time/residue: 0.2074 time to fit residues: 23.7251 Evaluate side-chains 87 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 80 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain B residue 46 ASN Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 307 VAL 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: 0.9990 chunk 59 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 31 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 6 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1613 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= 0.167 Angle : 0.520 8.200 7504 Z= 0.241 Chirality : 0.032 0.182 788 Planarity : 0.003 0.024 914 Dihedral : 8.570 88.698 728 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.22 % Allowed : 13.07 % Favored : 85.71 % 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: 3.68 (0.31), residues: 614 helix: 3.08 (0.20), residues: 528 sheet: None (None), residues: 0 loop : -2.19 (0.54), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 192 HIS 0.005 0.001 HIS A 283 PHE 0.021 0.001 PHE A 23 TYR 0.015 0.001 TYR A 198 ARG 0.002 0.000 ARG B 57 *********************** 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 95 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 88 time to evaluate : 0.617 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 93 average time/residue: 0.2009 time to fit residues: 23.6176 Evaluate side-chains 89 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 83 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain B residue 46 ASN Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 307 VAL 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: 0.9980 chunk 50 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 23 optimal weight: 8.9990 chunk 35 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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: 0.8077 moved from start: 0.1680 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 : 0.540 8.722 7504 Z= 0.252 Chirality : 0.033 0.172 788 Planarity : 0.003 0.024 914 Dihedral : 8.433 85.283 728 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.74 % Allowed : 13.24 % Favored : 85.02 % 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: 3.63 (0.31), residues: 614 helix: 3.04 (0.20), residues: 528 sheet: None (None), residues: 0 loop : -2.19 (0.54), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 192 HIS 0.005 0.001 HIS A 283 PHE 0.023 0.001 PHE B 23 TYR 0.015 0.002 TYR B 198 ARG 0.002 0.000 ARG B 57 *********************** 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 97 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 87 time to evaluate : 0.622 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 94 average time/residue: 0.2026 time to fit residues: 24.0734 Evaluate side-chains 90 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 83 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain B residue 46 ASN Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 307 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 40 optimal weight: 0.0470 chunk 29 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 54 optimal weight: 8.9990 chunk 57 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.6678 ------------------------------------------------------------------------------- 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: 0.8053 moved from start: 0.1755 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= 0.162 Angle : 0.547 9.679 7504 Z= 0.253 Chirality : 0.032 0.169 788 Planarity : 0.003 0.024 914 Dihedral : 8.213 80.559 728 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.74 % Allowed : 12.37 % Favored : 85.89 % 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: 3.74 (0.31), residues: 614 helix: 3.09 (0.20), residues: 528 sheet: None (None), residues: 0 loop : -1.98 (0.56), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 192 HIS 0.005 0.001 HIS B 283 PHE 0.023 0.001 PHE B 23 TYR 0.016 0.001 TYR B 198 ARG 0.002 0.000 ARG A 57 *********************** 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 100 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 90 time to evaluate : 0.634 Fit side-chains REVERT: A 36 LYS cc_start: 0.7729 (mmtm) cc_final: 0.7417 (mmtm) REVERT: B 36 LYS cc_start: 0.7731 (mmtm) cc_final: 0.7417 (mmtm) outliers start: 10 outliers final: 9 residues processed: 97 average time/residue: 0.2161 time to fit residues: 26.2489 Evaluate side-chains 96 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 87 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 94 PHE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain B residue 46 ASN Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 307 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 58 optimal weight: 0.4980 chunk 35 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.8059 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5552 Z= 0.173 Angle : 0.561 11.758 7504 Z= 0.259 Chirality : 0.033 0.157 788 Planarity : 0.003 0.024 914 Dihedral : 7.999 73.343 728 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.74 % Allowed : 12.37 % Favored : 85.89 % 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: 3.72 (0.31), residues: 614 helix: 3.08 (0.20), residues: 528 sheet: None (None), residues: 0 loop : -2.01 (0.56), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 192 HIS 0.005 0.001 HIS A 283 PHE 0.025 0.001 PHE B 23 TYR 0.016 0.001 TYR A 198 ARG 0.004 0.000 ARG A 57 *********************** 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 101 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 91 time to evaluate : 0.614 Fit side-chains REVERT: A 59 GLN cc_start: 0.6617 (pt0) cc_final: 0.6357 (pt0) outliers start: 10 outliers final: 8 residues processed: 98 average time/residue: 0.2078 time to fit residues: 25.5229 Evaluate side-chains 92 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 84 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 94 PHE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain B residue 46 ASN Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 307 VAL 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: 0.9990 chunk 5 optimal weight: 2.9990 chunk 37 optimal weight: 0.2980 chunk 30 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5552 Z= 0.181 Angle : 0.560 11.946 7504 Z= 0.260 Chirality : 0.033 0.153 788 Planarity : 0.003 0.024 914 Dihedral : 7.949 73.150 728 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.39 % Allowed : 13.07 % Favored : 85.54 % 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: 3.71 (0.31), residues: 614 helix: 3.07 (0.20), residues: 528 sheet: None (None), residues: 0 loop : -1.98 (0.56), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 192 HIS 0.005 0.001 HIS A 283 PHE 0.027 0.001 PHE A 23 TYR 0.016 0.001 TYR B 198 ARG 0.004 0.000 ARG B 57 ********************** 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 94 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 86 time to evaluate : 0.620 Fit side-chains REVERT: A 36 LYS cc_start: 0.7706 (mmtm) cc_final: 0.7456 (mmtm) REVERT: A 59 GLN cc_start: 0.6709 (pt0) cc_final: 0.6450 (pt0) REVERT: B 36 LYS cc_start: 0.7715 (mmtm) cc_final: 0.7457 (mmtm) outliers start: 8 outliers final: 8 residues processed: 92 average time/residue: 0.2089 time to fit residues: 24.1562 Evaluate side-chains 92 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 84 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 94 PHE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain B residue 46 ASN Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 307 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 0.0070 chunk 49 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 0.0270 chunk 43 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.165120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.110297 restraints weight = 6093.694| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.62 r_work: 0.3078 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 5552 Z= 0.145 Angle : 0.530 12.174 7504 Z= 0.246 Chirality : 0.031 0.147 788 Planarity : 0.003 0.025 914 Dihedral : 7.655 67.262 728 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.39 % Allowed : 13.24 % Favored : 85.37 % 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: 3.81 (0.31), residues: 614 helix: 3.15 (0.20), residues: 530 sheet: None (None), residues: 0 loop : -2.15 (0.55), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 192 HIS 0.004 0.001 HIS B 283 PHE 0.022 0.001 PHE A 23 TYR 0.017 0.001 TYR B 198 ARG 0.004 0.000 ARG B 57 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1533.22 seconds wall clock time: 28 minutes 24.60 seconds (1704.60 seconds total)