Starting phenix.real_space_refine (version: dev) on Sat Feb 18 12:26:07 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr0_30443/02_2023/7cr0_30443.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr0_30443/02_2023/7cr0_30443.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr0_30443/02_2023/7cr0_30443.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr0_30443/02_2023/7cr0_30443.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr0_30443/02_2023/7cr0_30443.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr0_30443/02_2023/7cr0_30443.pdb" } resolution = 3.1 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= 0.003 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 Process input model Symmetric amino acids flipped Residue "A GLU 117": "OE1" <-> "OE2" Residue "A GLU 257": "OE1" <-> "OE2" Residue "A GLU 322": "OE1" <-> "OE2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "B GLU 117": "OE1" <-> "OE2" Residue "B GLU 257": "OE1" <-> "OE2" Residue "B GLU 322": "OE1" <-> "OE2" Residue "B GLU 330": "OE1" <-> "OE2" Residue "C GLU 117": "OE1" <-> "OE2" Residue "C GLU 257": "OE1" <-> "OE2" Residue "C GLU 322": "OE1" <-> "OE2" Residue "C GLU 330": "OE1" <-> "OE2" Residue "D GLU 117": "OE1" <-> "OE2" Residue "D GLU 257": "OE1" <-> "OE2" Residue "D GLU 322": "OE1" <-> "OE2" Residue "D GLU 330": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 8188 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 2047 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 4, 'TRANS': 246} Chain breaks: 1 Chain: "B" Number of atoms: 2047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 2047 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 4, 'TRANS': 246} Chain breaks: 1 Chain: "C" Number of atoms: 2047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 2047 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 4, 'TRANS': 246} Chain breaks: 1 Chain: "D" Number of atoms: 2047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 2047 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 4, 'TRANS': 246} Chain breaks: 1 Time building chain proxies: 4.58, per 1000 atoms: 0.56 Number of scatterers: 8188 At special positions: 0 Unit cell: (132.834, 132.834, 77.064, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 1336 8.00 N 1380 7.00 C 5436 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: 3.08 Conformation dependent library (CDL) restraints added in 1.1 seconds 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1856 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 0 sheets defined 85.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 70 through 86 Processing helix chain 'A' and resid 91 through 114 removed outlier: 4.178A pdb=" N TYR A 95 " --> pdb=" O TRP A 91 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR A 114 " --> pdb=" O SER A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 148 removed outlier: 4.715A pdb=" N ILE A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 165 Processing helix chain 'A' and resid 166 through 183 Processing helix chain 'A' and resid 196 through 211 Processing helix chain 'A' and resid 215 through 228 Processing helix chain 'A' and resid 228 through 254 Processing helix chain 'A' and resid 263 through 276 removed outlier: 3.570A pdb=" N ALA A 267 " --> pdb=" O THR A 263 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR A 276 " --> pdb=" O LEU A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 330 removed outlier: 3.718A pdb=" N ARG A 291 " --> pdb=" O THR A 287 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THR A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N SER A 303 " --> pdb=" O LEU A 299 " (cutoff:3.500A) Proline residue: A 308 - end of helix removed outlier: 4.105A pdb=" N GLU A 330 " --> pdb=" O GLN A 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 86 Processing helix chain 'B' and resid 91 through 114 removed outlier: 4.178A pdb=" N TYR B 95 " --> pdb=" O TRP B 91 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR B 114 " --> pdb=" O SER B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 148 removed outlier: 4.715A pdb=" N ILE B 128 " --> pdb=" O GLY B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 165 Processing helix chain 'B' and resid 166 through 183 Processing helix chain 'B' and resid 196 through 211 Processing helix chain 'B' and resid 215 through 228 Processing helix chain 'B' and resid 228 through 254 Processing helix chain 'B' and resid 263 through 276 removed outlier: 3.570A pdb=" N ALA B 267 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR B 276 " --> pdb=" O LEU B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 330 removed outlier: 3.718A pdb=" N ARG B 291 " --> pdb=" O THR B 287 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N THR B 296 " --> pdb=" O LEU B 292 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N SER B 303 " --> pdb=" O LEU B 299 " (cutoff:3.500A) Proline residue: B 308 - end of helix removed outlier: 4.105A pdb=" N GLU B 330 " --> pdb=" O GLN B 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 86 Processing helix chain 'C' and resid 91 through 114 removed outlier: 4.177A pdb=" N TYR C 95 " --> pdb=" O TRP C 91 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR C 114 " --> pdb=" O SER C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 148 removed outlier: 4.715A pdb=" N ILE C 128 " --> pdb=" O GLY C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 165 Processing helix chain 'C' and resid 166 through 183 Processing helix chain 'C' and resid 196 through 211 Processing helix chain 'C' and resid 215 through 228 Processing helix chain 'C' and resid 228 through 254 Processing helix chain 'C' and resid 263 through 276 removed outlier: 3.570A pdb=" N ALA C 267 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR C 276 " --> pdb=" O LEU C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 330 removed outlier: 3.718A pdb=" N ARG C 291 " --> pdb=" O THR C 287 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N THR C 296 " --> pdb=" O LEU C 292 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU C 299 " --> pdb=" O ALA C 295 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N SER C 303 " --> pdb=" O LEU C 299 " (cutoff:3.500A) Proline residue: C 308 - end of helix removed outlier: 4.105A pdb=" N GLU C 330 " --> pdb=" O GLN C 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 86 Processing helix chain 'D' and resid 91 through 114 removed outlier: 4.178A pdb=" N TYR D 95 " --> pdb=" O TRP D 91 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR D 114 " --> pdb=" O SER D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 148 removed outlier: 4.715A pdb=" N ILE D 128 " --> pdb=" O GLY D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 165 Processing helix chain 'D' and resid 166 through 183 Processing helix chain 'D' and resid 196 through 211 Processing helix chain 'D' and resid 215 through 228 Processing helix chain 'D' and resid 228 through 254 Processing helix chain 'D' and resid 263 through 276 removed outlier: 3.570A pdb=" N ALA D 267 " --> pdb=" O THR D 263 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR D 276 " --> pdb=" O LEU D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 330 removed outlier: 3.718A pdb=" N ARG D 291 " --> pdb=" O THR D 287 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THR D 296 " --> pdb=" O LEU D 292 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU D 299 " --> pdb=" O ALA D 295 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N SER D 303 " --> pdb=" O LEU D 299 " (cutoff:3.500A) Proline residue: D 308 - end of helix removed outlier: 4.105A pdb=" N GLU D 330 " --> pdb=" O GLN D 326 " (cutoff:3.500A) 645 hydrogen bonds defined for protein. 1935 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: 2.07 Time building geometry restraints manager: 3.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2480 1.34 - 1.46: 2350 1.46 - 1.58: 3534 1.58 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 8412 Sorted by residual: bond pdb=" CD2 TYR B 280 " pdb=" CE2 TYR B 280 " ideal model delta sigma weight residual 1.382 1.352 0.030 3.00e-02 1.11e+03 9.69e-01 bond pdb=" CD2 TYR D 280 " pdb=" CE2 TYR D 280 " ideal model delta sigma weight residual 1.382 1.352 0.030 3.00e-02 1.11e+03 9.69e-01 bond pdb=" CD2 TYR A 280 " pdb=" CE2 TYR A 280 " ideal model delta sigma weight residual 1.382 1.352 0.030 3.00e-02 1.11e+03 9.69e-01 bond pdb=" CD2 TYR C 280 " pdb=" CE2 TYR C 280 " ideal model delta sigma weight residual 1.382 1.352 0.030 3.00e-02 1.11e+03 9.69e-01 bond pdb=" CB THR C 274 " pdb=" CG2 THR C 274 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.60e-01 ... (remaining 8407 not shown) Histogram of bond angle deviations from ideal: 99.11 - 106.10: 72 106.10 - 113.08: 4504 113.08 - 120.07: 3608 120.07 - 127.06: 3100 127.06 - 134.04: 104 Bond angle restraints: 11388 Sorted by residual: angle pdb=" N ARG B 87 " pdb=" CA ARG B 87 " pdb=" C ARG B 87 " ideal model delta sigma weight residual 109.81 114.52 -4.71 2.21e+00 2.05e-01 4.54e+00 angle pdb=" N ARG C 87 " pdb=" CA ARG C 87 " pdb=" C ARG C 87 " ideal model delta sigma weight residual 109.81 114.52 -4.71 2.21e+00 2.05e-01 4.54e+00 angle pdb=" N ARG D 87 " pdb=" CA ARG D 87 " pdb=" C ARG D 87 " ideal model delta sigma weight residual 109.81 114.52 -4.71 2.21e+00 2.05e-01 4.54e+00 angle pdb=" N ARG A 87 " pdb=" CA ARG A 87 " pdb=" C ARG A 87 " ideal model delta sigma weight residual 109.81 114.52 -4.71 2.21e+00 2.05e-01 4.54e+00 angle pdb=" C ASP A 212 " pdb=" N ARG A 213 " pdb=" CA ARG A 213 " ideal model delta sigma weight residual 121.54 125.46 -3.92 1.91e+00 2.74e-01 4.22e+00 ... (remaining 11383 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 4272 17.87 - 35.74: 428 35.74 - 53.61: 80 53.61 - 71.48: 8 71.48 - 89.35: 4 Dihedral angle restraints: 4792 sinusoidal: 1884 harmonic: 2908 Sorted by residual: dihedral pdb=" CA GLU A 86 " pdb=" C GLU A 86 " pdb=" N ARG A 87 " pdb=" CA ARG A 87 " ideal model delta harmonic sigma weight residual -180.00 -160.39 -19.61 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA GLU D 86 " pdb=" C GLU D 86 " pdb=" N ARG D 87 " pdb=" CA ARG D 87 " ideal model delta harmonic sigma weight residual 180.00 -160.42 -19.58 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA GLU C 86 " pdb=" C GLU C 86 " pdb=" N ARG C 87 " pdb=" CA ARG C 87 " ideal model delta harmonic sigma weight residual 180.00 -160.42 -19.58 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 4789 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 712 0.031 - 0.063: 422 0.063 - 0.094: 90 0.094 - 0.125: 20 0.125 - 0.157: 8 Chirality restraints: 1252 Sorted by residual: chirality pdb=" CA ARG B 87 " pdb=" N ARG B 87 " pdb=" C ARG B 87 " pdb=" CB ARG B 87 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.14e-01 chirality pdb=" CA ARG C 87 " pdb=" N ARG C 87 " pdb=" C ARG C 87 " pdb=" CB ARG C 87 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.14e-01 chirality pdb=" CA ARG D 87 " pdb=" N ARG D 87 " pdb=" C ARG D 87 " pdb=" CB ARG D 87 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.14e-01 ... (remaining 1249 not shown) Planarity restraints: 1380 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 298 " 0.008 2.00e-02 2.50e+03 1.60e-02 2.55e+00 pdb=" C THR A 298 " -0.028 2.00e-02 2.50e+03 pdb=" O THR A 298 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU A 299 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 298 " 0.008 2.00e-02 2.50e+03 1.60e-02 2.55e+00 pdb=" C THR D 298 " -0.028 2.00e-02 2.50e+03 pdb=" O THR D 298 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU D 299 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 298 " -0.008 2.00e-02 2.50e+03 1.60e-02 2.55e+00 pdb=" C THR B 298 " 0.028 2.00e-02 2.50e+03 pdb=" O THR B 298 " -0.010 2.00e-02 2.50e+03 pdb=" N LEU B 299 " -0.009 2.00e-02 2.50e+03 ... (remaining 1377 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1403 2.75 - 3.29: 7751 3.29 - 3.82: 13206 3.82 - 4.36: 15284 4.36 - 4.90: 26020 Nonbonded interactions: 63664 Sorted by model distance: nonbonded pdb=" OE1 GLU C 86 " pdb=" NH2 ARG C 214 " model vdw 2.212 2.520 nonbonded pdb=" OE1 GLU D 86 " pdb=" NH2 ARG D 214 " model vdw 2.212 2.520 nonbonded pdb=" OE1 GLU A 86 " pdb=" NH2 ARG A 214 " model vdw 2.212 2.520 nonbonded pdb=" OE1 GLU B 86 " pdb=" NH2 ARG B 214 " model vdw 2.212 2.520 nonbonded pdb=" O SER B 110 " pdb=" NH2 ARG B 201 " model vdw 2.262 2.520 ... (remaining 63659 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 5436 2.51 5 N 1380 2.21 5 O 1336 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: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.990 Check model and map are aligned: 0.100 Process input model: 22.660 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.090 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.032 8412 Z= 0.327 Angle : 0.627 5.250 11388 Z= 0.378 Chirality : 0.040 0.157 1252 Planarity : 0.005 0.029 1380 Dihedral : 14.379 89.345 2936 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % 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: -4.99 (0.17), residues: 988 helix: -2.96 (0.11), residues: 824 sheet: None (None), residues: 0 loop : -3.65 (0.39), residues: 164 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 0.991 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.2292 time to fit residues: 50.3050 Evaluate side-chains 150 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 0.919 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 chunk 42 optimal weight: 0.8980 chunk 25 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 58 optimal weight: 8.9990 chunk 90 optimal weight: 0.5980 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 78 GLN A 79 ASN A 228 HIS A 323 GLN ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 GLN B 228 HIS B 323 GLN ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 GLN C 228 HIS C 323 GLN ** C 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 GLN D 79 ASN D 228 HIS D 323 GLN ** D 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.019 8412 Z= 0.169 Angle : 0.511 5.146 11388 Z= 0.285 Chirality : 0.035 0.115 1252 Planarity : 0.004 0.023 1380 Dihedral : 4.158 12.702 1124 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer Outliers : 2.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.23), residues: 988 helix: 0.04 (0.16), residues: 824 sheet: None (None), residues: 0 loop : -2.91 (0.40), residues: 164 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 161 time to evaluate : 0.956 Fit side-chains outliers start: 24 outliers final: 16 residues processed: 173 average time/residue: 0.1934 time to fit residues: 45.9683 Evaluate side-chains 163 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 147 time to evaluate : 0.943 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.0730 time to fit residues: 3.3461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 75 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 90 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 GLN ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 323 GLN ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 GLN ** C 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 323 GLN ** D 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.035 8412 Z= 0.351 Angle : 0.584 5.265 11388 Z= 0.318 Chirality : 0.040 0.132 1252 Planarity : 0.003 0.024 1380 Dihedral : 4.108 12.823 1124 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer Outliers : 1.55 % 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: 0.73 (0.26), residues: 988 helix: 1.16 (0.18), residues: 832 sheet: None (None), residues: 0 loop : -3.19 (0.38), residues: 156 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 164 time to evaluate : 0.892 Fit side-chains outliers start: 13 outliers final: 8 residues processed: 168 average time/residue: 0.2162 time to fit residues: 48.5924 Evaluate side-chains 171 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 163 time to evaluate : 0.920 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0817 time to fit residues: 2.5999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 96 optimal weight: 0.9980 chunk 86 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 54 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 GLN ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 323 GLN ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 GLN ** C 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 323 GLN ** D 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.015 8412 Z= 0.153 Angle : 0.470 5.645 11388 Z= 0.256 Chirality : 0.035 0.112 1252 Planarity : 0.003 0.026 1380 Dihedral : 3.736 11.060 1124 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer Outliers : 2.02 % 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: 1.61 (0.27), residues: 988 helix: 1.77 (0.18), residues: 832 sheet: None (None), residues: 0 loop : -2.88 (0.40), residues: 156 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 156 time to evaluate : 0.834 Fit side-chains outliers start: 17 outliers final: 13 residues processed: 169 average time/residue: 0.1795 time to fit residues: 41.9640 Evaluate side-chains 165 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 152 time to evaluate : 0.958 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0749 time to fit residues: 3.0647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 82 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 chunk 86 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 87 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 GLN B 323 GLN C 323 GLN ** D 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 323 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.024 8412 Z= 0.245 Angle : 0.526 6.546 11388 Z= 0.281 Chirality : 0.038 0.121 1252 Planarity : 0.003 0.031 1380 Dihedral : 3.776 11.740 1124 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer Outliers : 1.79 % 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: 1.94 (0.27), residues: 988 helix: 1.98 (0.18), residues: 832 sheet: None (None), residues: 0 loop : -2.72 (0.41), residues: 156 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 142 time to evaluate : 0.926 Fit side-chains outliers start: 15 outliers final: 3 residues processed: 153 average time/residue: 0.1936 time to fit residues: 40.7681 Evaluate side-chains 138 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 135 time to evaluate : 0.938 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0762 time to fit residues: 1.7257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.3980 chunk 56 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 80 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 8 optimal weight: 6.9990 chunk 32 optimal weight: 9.9990 chunk 50 optimal weight: 10.0000 chunk 93 optimal weight: 0.0170 chunk 10 optimal weight: 0.9990 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 GLN B 323 GLN C 323 GLN ** D 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 323 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.017 8412 Z= 0.146 Angle : 0.475 7.120 11388 Z= 0.249 Chirality : 0.035 0.110 1252 Planarity : 0.002 0.022 1380 Dihedral : 3.587 11.041 1124 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer Outliers : 1.90 % 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: 2.29 (0.27), residues: 988 helix: 2.22 (0.18), residues: 832 sheet: None (None), residues: 0 loop : -2.58 (0.42), residues: 156 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 156 time to evaluate : 0.833 Fit side-chains outliers start: 16 outliers final: 8 residues processed: 168 average time/residue: 0.2036 time to fit residues: 45.7699 Evaluate side-chains 157 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 149 time to evaluate : 0.822 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0725 time to fit residues: 2.2658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 6.9990 chunk 70 optimal weight: 0.0980 chunk 54 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 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 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 GLN B 323 GLN C 323 GLN ** D 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 323 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.018 8412 Z= 0.156 Angle : 0.488 8.187 11388 Z= 0.252 Chirality : 0.035 0.114 1252 Planarity : 0.002 0.019 1380 Dihedral : 3.497 10.780 1124 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer Outliers : 2.02 % 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: 2.47 (0.27), residues: 988 helix: 2.33 (0.18), residues: 832 sheet: None (None), residues: 0 loop : -2.45 (0.44), residues: 156 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 150 time to evaluate : 0.963 Fit side-chains outliers start: 17 outliers final: 6 residues processed: 167 average time/residue: 0.1972 time to fit residues: 45.1368 Evaluate side-chains 151 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 145 time to evaluate : 0.812 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0702 time to fit residues: 1.9011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 65 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 8 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 chunk 87 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 84 optimal weight: 0.1980 chunk 89 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 GLN B 323 GLN C 323 GLN ** D 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 323 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.020 8412 Z= 0.165 Angle : 0.488 8.809 11388 Z= 0.253 Chirality : 0.035 0.112 1252 Planarity : 0.002 0.020 1380 Dihedral : 3.487 10.732 1124 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer Outliers : 0.83 % 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: 2.53 (0.27), residues: 988 helix: 2.37 (0.17), residues: 832 sheet: None (None), residues: 0 loop : -2.43 (0.44), residues: 156 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 155 time to evaluate : 0.944 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 162 average time/residue: 0.1980 time to fit residues: 44.0371 Evaluate side-chains 153 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 150 time to evaluate : 0.929 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3874 time to fit residues: 2.6637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 0.9980 chunk 54 optimal weight: 0.0370 chunk 39 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 84 optimal weight: 0.0050 chunk 89 optimal weight: 3.9990 chunk 58 optimal weight: 7.9990 chunk 94 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 overall best weight: 0.5474 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 GLN B 323 GLN C 323 GLN ** D 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 323 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.020 8412 Z= 0.136 Angle : 0.495 9.315 11388 Z= 0.250 Chirality : 0.034 0.109 1252 Planarity : 0.002 0.020 1380 Dihedral : 3.408 10.682 1124 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % 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: 2.67 (0.27), residues: 988 helix: 2.46 (0.17), residues: 832 sheet: None (None), residues: 0 loop : -2.36 (0.45), residues: 156 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 1.003 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.1824 time to fit residues: 40.8508 Evaluate side-chains 152 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 1.021 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 79 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 84 optimal weight: 0.0980 chunk 24 optimal weight: 4.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 GLN B 323 GLN C 323 GLN ** D 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 323 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 8412 Z= 0.157 Angle : 0.516 9.444 11388 Z= 0.266 Chirality : 0.035 0.111 1252 Planarity : 0.002 0.020 1380 Dihedral : 3.402 10.555 1124 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer Outliers : 0.24 % 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: 2.73 (0.27), residues: 988 helix: 2.50 (0.17), residues: 832 sheet: None (None), residues: 0 loop : -2.32 (0.45), residues: 156 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 144 time to evaluate : 0.888 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 146 average time/residue: 0.1893 time to fit residues: 38.8146 Evaluate side-chains 143 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 142 time to evaluate : 0.983 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0770 time to fit residues: 1.4460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 22 optimal weight: 0.4980 chunk 79 optimal weight: 0.0270 chunk 33 optimal weight: 8.9990 chunk 81 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 57 optimal weight: 0.2980 overall best weight: 0.7640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 GLN B 323 GLN C 323 GLN ** D 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 323 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.158444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.112147 restraints weight = 10348.724| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.96 r_work: 0.3223 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 8412 Z= 0.161 Angle : 0.524 9.724 11388 Z= 0.267 Chirality : 0.035 0.111 1252 Planarity : 0.002 0.019 1380 Dihedral : 3.399 10.598 1124 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer Outliers : 0.12 % 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: 2.81 (0.27), residues: 988 helix: 2.56 (0.17), residues: 832 sheet: None (None), residues: 0 loop : -2.32 (0.45), residues: 156 =============================================================================== Job complete usr+sys time: 1913.03 seconds wall clock time: 35 minutes 17.49 seconds (2117.49 seconds total)