Starting phenix.real_space_refine (version: dev) on Tue Nov 29 12:12:09 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qev_13942/11_2022/7qev_13942_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qev_13942/11_2022/7qev_13942.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qev_13942/11_2022/7qev_13942.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qev_13942/11_2022/7qev_13942.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qev_13942/11_2022/7qev_13942_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qev_13942/11_2022/7qev_13942_updated.pdb" } resolution = 2.9 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ASP 2": "OD1" <-> "OD2" Residue "A PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 47": "OE1" <-> "OE2" Residue "A PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 159": "OD1" <-> "OD2" Residue "A PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 187": "OE1" <-> "OE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 47": "OE1" <-> "OE2" Residue "B ASP 50": "OD1" <-> "OD2" Residue "B PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 147": "OE1" <-> "OE2" Residue "B TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 187": "OE1" <-> "OE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 3204 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1577 Classifications: {'peptide': 193} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 186} Chain breaks: 1 Chain: "B" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1548 Classifications: {'peptide': 190} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 183} Chain breaks: 1 Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 37 Unusual residues: {'LMT': 3, 'PTY': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {'LMT': 3, 'PTY': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Time building chain proxies: 2.37, per 1000 atoms: 0.74 Number of scatterers: 3204 At special positions: 0 Unit cell: (71.94, 64.31, 92.65, 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 30 16.00 O 529 8.00 N 504 7.00 C 2141 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS A 180 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 174 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 169 " distance=2.03 Simple disulfide: pdb=" SG CYS B 53 " - pdb=" SG CYS B 180 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 174 " distance=2.03 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 169 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.34 Conformation dependent library (CDL) restraints added in 460.9 milliseconds 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 730 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 16 helices and 2 sheets defined 69.2% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 6 through 13 Processing helix chain 'A' and resid 19 through 38 removed outlier: 3.548A pdb=" N ILE A 23 " --> pdb=" O SER A 19 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LEU A 25 " --> pdb=" O GLY A 21 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N THR A 26 " --> pdb=" O LYS A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 42 No H-bonds generated for 'chain 'A' and resid 40 through 42' Processing helix chain 'A' and resid 44 through 46 No H-bonds generated for 'chain 'A' and resid 44 through 46' Processing helix chain 'A' and resid 60 through 68 Processing helix chain 'A' and resid 73 through 94 Proline residue: A 87 - end of helix Processing helix chain 'A' and resid 96 through 102 Processing helix chain 'A' and resid 130 through 158 removed outlier: 3.816A pdb=" N TRP A 134 " --> pdb=" O GLY A 130 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL A 144 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A 145 " --> pdb=" O PHE A 141 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR A 155 " --> pdb=" O MET A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 215 removed outlier: 3.614A pdb=" N GLU A 209 " --> pdb=" O LEU A 205 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU A 210 " --> pdb=" O ASN A 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 14 Processing helix chain 'B' and resid 19 through 38 removed outlier: 4.263A pdb=" N LEU B 25 " --> pdb=" O GLY B 21 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N THR B 26 " --> pdb=" O LYS B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 46 removed outlier: 4.084A pdb=" N TRP B 44 " --> pdb=" O LYS B 41 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY B 45 " --> pdb=" O GLU B 42 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ASP B 46 " --> pdb=" O VAL B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 68 Processing helix chain 'B' and resid 73 through 100 Proline residue: B 87 - end of helix removed outlier: 3.564A pdb=" N VAL B 91 " --> pdb=" O PRO B 87 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA B 92 " --> pdb=" O ALA B 88 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA B 96 " --> pdb=" O ALA B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 158 removed outlier: 3.585A pdb=" N ILE B 140 " --> pdb=" O TYR B 136 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE B 145 " --> pdb=" O PHE B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 216 removed outlier: 4.012A pdb=" N ARG B 216 " --> pdb=" O TYR B 212 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 166 through 169 Processing sheet with id= B, first strand: chain 'B' and resid 166 through 169 186 hydrogen bonds defined for protein. 549 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.83 Time building geometry restraints manager: 1.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 927 1.34 - 1.46: 689 1.46 - 1.57: 1618 1.57 - 1.69: 0 1.69 - 1.80: 44 Bond restraints: 3278 Sorted by residual: bond pdb=" C7 LMT A 303 " pdb=" C8 LMT A 303 " ideal model delta sigma weight residual 1.489 1.568 -0.079 2.50e-02 1.60e+03 1.01e+01 bond pdb=" C7 LMT A 302 " pdb=" C8 LMT A 302 " ideal model delta sigma weight residual 1.489 1.567 -0.078 2.50e-02 1.60e+03 9.72e+00 bond pdb=" C7 LMT B 302 " pdb=" C8 LMT B 302 " ideal model delta sigma weight residual 1.489 1.566 -0.077 2.50e-02 1.60e+03 9.48e+00 bond pdb=" C2 LMT B 302 " pdb=" C3 LMT B 302 " ideal model delta sigma weight residual 1.493 1.563 -0.070 2.30e-02 1.89e+03 9.30e+00 bond pdb=" C7 LMT A 301 " pdb=" C8 LMT A 301 " ideal model delta sigma weight residual 1.489 1.565 -0.076 2.50e-02 1.60e+03 9.21e+00 ... (remaining 3273 not shown) Histogram of bond angle deviations from ideal: 99.90 - 106.72: 79 106.72 - 113.54: 1887 113.54 - 120.36: 1253 120.36 - 127.18: 1161 127.18 - 134.00: 49 Bond angle restraints: 4429 Sorted by residual: angle pdb=" C1 LMT A 301 " pdb=" C2 LMT A 301 " pdb=" C3 LMT A 301 " ideal model delta sigma weight residual 116.40 109.79 6.61 2.18e+00 2.10e-01 9.18e+00 angle pdb=" C1 LMT B 302 " pdb=" C2 LMT B 302 " pdb=" C3 LMT B 302 " ideal model delta sigma weight residual 116.40 109.97 6.43 2.18e+00 2.10e-01 8.68e+00 angle pdb=" C TRP B 172 " pdb=" N PRO B 173 " pdb=" CA PRO B 173 " ideal model delta sigma weight residual 127.00 132.66 -5.66 2.40e+00 1.74e-01 5.57e+00 angle pdb=" N ASN A 176 " pdb=" CA ASN A 176 " pdb=" CB ASN A 176 " ideal model delta sigma weight residual 110.49 106.52 3.97 1.69e+00 3.50e-01 5.51e+00 angle pdb=" C TRP A 172 " pdb=" N PRO A 173 " pdb=" CA PRO A 173 " ideal model delta sigma weight residual 127.00 132.53 -5.53 2.40e+00 1.74e-01 5.32e+00 ... (remaining 4424 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 1704 17.88 - 35.76: 167 35.76 - 53.64: 24 53.64 - 71.52: 3 71.52 - 89.40: 1 Dihedral angle restraints: 1899 sinusoidal: 772 harmonic: 1127 Sorted by residual: dihedral pdb=" CA PRO B 175 " pdb=" C PRO B 175 " pdb=" N ASN B 176 " pdb=" CA ASN B 176 " ideal model delta harmonic sigma weight residual 180.00 -157.45 -22.55 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA ILE B 23 " pdb=" C ILE B 23 " pdb=" N TRP B 24 " pdb=" CA TRP B 24 " ideal model delta harmonic sigma weight residual -180.00 -158.55 -21.45 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA PRO A 175 " pdb=" C PRO A 175 " pdb=" N ASN A 176 " pdb=" CA ASN A 176 " ideal model delta harmonic sigma weight residual -180.00 -159.14 -20.86 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 1896 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 209 0.029 - 0.058: 203 0.058 - 0.088: 58 0.088 - 0.117: 20 0.117 - 0.146: 7 Chirality restraints: 497 Sorted by residual: chirality pdb=" CA THR A 86 " pdb=" N THR A 86 " pdb=" C THR A 86 " pdb=" CB THR A 86 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.32e-01 chirality pdb=" CA PRO B 185 " pdb=" N PRO B 185 " pdb=" C PRO B 185 " pdb=" CB PRO B 185 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.59e-01 chirality pdb=" CA THR B 86 " pdb=" N THR B 86 " pdb=" C THR B 86 " pdb=" CB THR B 86 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.13 2.00e-01 2.50e+01 4.25e-01 ... (remaining 494 not shown) Planarity restraints: 526 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 174 " 0.019 5.00e-02 4.00e+02 2.93e-02 1.37e+00 pdb=" N PRO A 175 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 175 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 175 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 176 " 0.006 2.00e-02 2.50e+03 1.16e-02 1.34e+00 pdb=" CG ASN A 176 " -0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN A 176 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN A 176 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 86 " 0.017 5.00e-02 4.00e+02 2.61e-02 1.09e+00 pdb=" N PRO A 87 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO A 87 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 87 " 0.015 5.00e-02 4.00e+02 ... (remaining 523 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 126 2.71 - 3.26: 3341 3.26 - 3.81: 4916 3.81 - 4.35: 5882 4.35 - 4.90: 9955 Nonbonded interactions: 24220 Sorted by model distance: nonbonded pdb=" O ILE B 71 " pdb=" OH TYR B 158 " model vdw 2.164 2.440 nonbonded pdb=" O ILE A 71 " pdb=" OH TYR A 158 " model vdw 2.167 2.440 nonbonded pdb=" O TYR B 152 " pdb=" O HOH B 401 " model vdw 2.211 2.440 nonbonded pdb=" O SER A 17 " pdb=" NZ LYS A 22 " model vdw 2.260 2.520 nonbonded pdb=" O THR A 18 " pdb=" N LYS A 22 " model vdw 2.261 2.520 ... (remaining 24215 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' and (resid 1 through 101 or resid 129 through 217 or (resid 301 and ( \ name C4 or name C5 or name C6 or name C7 )) or resid 302 through 304)) selection = (chain 'B' and (resid 1 through 217 or resid 301 or (resid 302 and (name C2 or n \ ame C3 or name C4 or name C5 or name C6 or name C7 or name C8 )) or resid 303 th \ rough 304)) } 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 30 5.16 5 C 2141 2.51 5 N 504 2.21 5 O 529 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: 0.270 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: 1.520 Check model and map are aligned: 0.050 Convert atoms to be neutral: 0.020 Process input model: 13.820 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 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 : 0.010 0.079 3278 Z= 0.682 Angle : 0.744 6.607 4429 Z= 0.382 Chirality : 0.046 0.146 497 Planarity : 0.003 0.029 526 Dihedral : 13.758 89.401 1151 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: -0.15 (0.42), residues: 375 helix: 0.22 (0.31), residues: 247 sheet: 0.19 (0.90), residues: 34 loop : -0.70 (0.66), residues: 94 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.382 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 1.1830 time to fit residues: 73.0235 Evaluate side-chains 45 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.366 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 22 optimal weight: 0.1980 chunk 34 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- 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: 0.8541 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 3278 Z= 0.217 Angle : 0.635 7.949 4429 Z= 0.326 Chirality : 0.041 0.131 497 Planarity : 0.004 0.028 526 Dihedral : 7.252 59.377 455 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer Outliers : 1.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.37 (0.44), residues: 375 helix: 1.64 (0.32), residues: 257 sheet: 0.23 (0.91), residues: 34 loop : -1.03 (0.72), residues: 84 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 53 time to evaluate : 0.381 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 56 average time/residue: 1.0659 time to fit residues: 61.6457 Evaluate side-chains 47 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 46 time to evaluate : 0.385 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.5073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 3278 Z= 0.181 Angle : 0.565 9.153 4429 Z= 0.287 Chirality : 0.040 0.167 497 Planarity : 0.003 0.025 526 Dihedral : 5.959 53.843 455 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer Outliers : 1.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.79 (0.45), residues: 375 helix: 2.09 (0.33), residues: 253 sheet: 0.36 (0.92), residues: 34 loop : -1.18 (0.68), residues: 88 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 54 time to evaluate : 0.410 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 58 average time/residue: 1.0201 time to fit residues: 61.2033 Evaluate side-chains 53 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 50 time to evaluate : 0.384 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 0.0394 time to fit residues: 0.5689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 16 optimal weight: 0.9990 chunk 23 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 18 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 20 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 27 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.027 3278 Z= 0.248 Angle : 0.603 8.633 4429 Z= 0.305 Chirality : 0.042 0.157 497 Planarity : 0.003 0.027 526 Dihedral : 5.740 49.594 455 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer Outliers : 1.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.96 (0.45), residues: 375 helix: 2.21 (0.33), residues: 253 sheet: 0.36 (0.93), residues: 34 loop : -1.08 (0.69), residues: 88 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 53 time to evaluate : 0.394 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 56 average time/residue: 1.1209 time to fit residues: 64.7183 Evaluate side-chains 52 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 49 time to evaluate : 0.388 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.5003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 15 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 18 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 33 optimal weight: 0.0980 chunk 7 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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: 0.8504 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 3278 Z= 0.161 Angle : 0.568 8.621 4429 Z= 0.281 Chirality : 0.040 0.167 497 Planarity : 0.003 0.029 526 Dihedral : 5.216 44.748 455 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer Outliers : 2.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.09 (0.45), residues: 375 helix: 2.29 (0.33), residues: 253 sheet: 0.82 (1.04), residues: 28 loop : -1.00 (0.65), residues: 94 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 53 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 2 residues processed: 61 average time/residue: 0.9585 time to fit residues: 60.5909 Evaluate side-chains 54 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 52 time to evaluate : 0.293 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.3901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 17 optimal weight: 0.1980 chunk 3 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 20.0000 chunk 35 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 20 optimal weight: 8.9990 chunk 26 optimal weight: 0.5980 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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: 0.8500 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 3278 Z= 0.168 Angle : 0.599 9.433 4429 Z= 0.294 Chirality : 0.041 0.164 497 Planarity : 0.003 0.027 526 Dihedral : 4.869 38.968 455 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer Outliers : 1.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.12 (0.45), residues: 375 helix: 2.30 (0.33), residues: 253 sheet: 0.92 (1.05), residues: 28 loop : -1.00 (0.65), residues: 94 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 55 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 59 average time/residue: 1.0142 time to fit residues: 61.8461 Evaluate side-chains 55 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 52 time to evaluate : 0.386 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.4967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 20 optimal weight: 7.9990 chunk 30 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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: 0.8497 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 3278 Z= 0.182 Angle : 0.609 8.832 4429 Z= 0.306 Chirality : 0.042 0.181 497 Planarity : 0.003 0.029 526 Dihedral : 4.780 34.671 455 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer Outliers : 1.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.16 (0.45), residues: 375 helix: 2.40 (0.33), residues: 248 sheet: 0.98 (1.05), residues: 28 loop : -1.02 (0.61), residues: 99 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 52 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 58 average time/residue: 1.0614 time to fit residues: 63.7649 Evaluate side-chains 55 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 52 time to evaluate : 0.358 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.4772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 18 optimal weight: 0.1980 chunk 3 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 33 optimal weight: 0.4980 chunk 35 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 34 optimal weight: 0.1980 chunk 20 optimal weight: 10.0000 chunk 14 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 10 optimal weight: 4.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 3278 Z= 0.145 Angle : 0.572 7.700 4429 Z= 0.285 Chirality : 0.041 0.171 497 Planarity : 0.003 0.028 526 Dihedral : 4.464 27.591 455 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer Outliers : 1.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.20 (0.44), residues: 375 helix: 2.47 (0.33), residues: 248 sheet: 1.09 (1.06), residues: 28 loop : -1.17 (0.58), residues: 99 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 52 time to evaluate : 0.366 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 55 average time/residue: 1.0861 time to fit residues: 61.6189 Evaluate side-chains 51 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 49 time to evaluate : 0.383 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.5079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 30 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 17 optimal weight: 0.3980 chunk 25 optimal weight: 0.9980 chunk 37 optimal weight: 9.9990 chunk 3 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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: 0.8497 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 3278 Z= 0.192 Angle : 0.603 8.421 4429 Z= 0.300 Chirality : 0.042 0.197 497 Planarity : 0.003 0.028 526 Dihedral : 4.474 24.722 455 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer Outliers : 0.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.18 (0.44), residues: 375 helix: 2.46 (0.33), residues: 248 sheet: 1.00 (1.05), residues: 28 loop : -1.16 (0.58), residues: 99 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 50 time to evaluate : 0.353 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 53 average time/residue: 1.0623 time to fit residues: 58.0797 Evaluate side-chains 52 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 50 time to evaluate : 0.330 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.4322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 23 optimal weight: 3.9990 chunk 32 optimal weight: 0.3980 chunk 9 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 4 optimal weight: 0.0570 chunk 8 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- 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: 0.8475 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 3278 Z= 0.153 Angle : 0.600 8.798 4429 Z= 0.296 Chirality : 0.041 0.194 497 Planarity : 0.003 0.028 526 Dihedral : 4.255 20.915 455 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer Outliers : 0.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.21 (0.44), residues: 375 helix: 2.49 (0.33), residues: 248 sheet: 1.13 (1.07), residues: 28 loop : -1.23 (0.57), residues: 99 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 55 time to evaluate : 0.386 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 57 average time/residue: 1.0194 time to fit residues: 60.0962 Evaluate side-chains 51 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 49 time to evaluate : 0.384 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.5079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 26 optimal weight: 2.9990 chunk 1 optimal weight: 9.9990 chunk 21 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 20 optimal weight: 0.0270 chunk 25 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.084921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.060814 restraints weight = 8925.339| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 2.58 r_work: 0.2945 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 2.33 restraints_weight: 0.2500 r_work: 0.2924 rms_B_bonded: 2.33 restraints_weight: 0.1250 r_work: 0.2914 rms_B_bonded: 2.36 restraints_weight: 0.0625 r_work: 0.2903 rms_B_bonded: 2.41 restraints_weight: 0.0312 r_work: 0.2893 rms_B_bonded: 2.49 restraints_weight: 0.0156 r_work: 0.2882 rms_B_bonded: 2.58 restraints_weight: 0.0078 r_work: 0.2871 rms_B_bonded: 2.69 restraints_weight: 0.0039 r_work: 0.2860 rms_B_bonded: 2.81 restraints_weight: 0.0020 r_work: 0.2849 rms_B_bonded: 2.95 restraints_weight: 0.0010 r_work: 0.2837 rms_B_bonded: 3.11 restraints_weight: 0.0005 r_work: 0.2825 rms_B_bonded: 3.29 restraints_weight: 0.0002 r_work: 0.2812 rms_B_bonded: 3.48 restraints_weight: 0.0001 r_work: 0.2799 rms_B_bonded: 3.70 restraints_weight: 0.0001 r_work: 0.2786 rms_B_bonded: 3.94 restraints_weight: 0.0000 r_work: 0.2772 rms_B_bonded: 4.20 restraints_weight: 0.0000 r_work: 0.2758 rms_B_bonded: 4.48 restraints_weight: 0.0000 r_work: 0.2743 rms_B_bonded: 4.79 restraints_weight: 0.0000 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 3278 Z= 0.173 Angle : 0.637 9.579 4429 Z= 0.310 Chirality : 0.041 0.198 497 Planarity : 0.003 0.028 526 Dihedral : 4.244 19.575 455 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer Outliers : 0.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.25 (0.44), residues: 375 helix: 2.54 (0.33), residues: 248 sheet: 1.13 (1.08), residues: 28 loop : -1.26 (0.56), residues: 99 =============================================================================== Job complete usr+sys time: 1505.01 seconds wall clock time: 27 minutes 36.32 seconds (1656.32 seconds total)