Starting phenix.real_space_refine on Thu Dec 7 17:20:54 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qev_13942/12_2023/7qev_13942_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qev_13942/12_2023/7qev_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_13942/12_2023/7qev_13942.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qev_13942/12_2023/7qev_13942.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qev_13942/12_2023/7qev_13942_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qev_13942/12_2023/7qev_13942_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 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. 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-1.21rc1-5172/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: 203 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: 206 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: 2.31, per 1000 atoms: 0.72 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: 1.08 Conformation dependent library (CDL) restraints added in 470.8 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: 0.55 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: 0.80 Time building geometry restraints manager: 1.19 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=" C1 LMT A 301 " pdb=" C2 LMT A 301 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.00e-02 2.50e+03 5.94e+00 bond pdb=" C1 LMT B 302 " pdb=" C2 LMT B 302 " ideal model delta sigma weight residual 1.516 1.564 -0.048 2.00e-02 2.50e+03 5.83e+00 bond pdb=" C7 LMT A 303 " pdb=" C8 LMT A 303 " ideal model delta sigma weight residual 1.529 1.568 -0.039 2.00e-02 2.50e+03 3.90e+00 bond pdb=" C7 LMT A 302 " pdb=" C8 LMT A 302 " ideal model delta sigma weight residual 1.529 1.567 -0.038 2.00e-02 2.50e+03 3.60e+00 bond pdb=" C7 LMT B 302 " pdb=" C8 LMT B 302 " ideal model delta sigma weight residual 1.529 1.566 -0.037 2.00e-02 2.50e+03 3.42e+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=" C6 LMT A 303 " pdb=" C7 LMT A 303 " pdb=" C8 LMT A 303 " ideal model delta sigma weight residual 117.26 109.10 8.16 3.00e+00 1.11e-01 7.41e+00 angle pdb=" C6 LMT A 301 " pdb=" C7 LMT A 301 " pdb=" C8 LMT A 301 " ideal model delta sigma weight residual 117.26 109.62 7.64 3.00e+00 1.11e-01 6.48e+00 angle pdb=" C6 LMT A 302 " pdb=" C7 LMT A 302 " pdb=" C8 LMT A 302 " ideal model delta sigma weight residual 117.26 109.64 7.62 3.00e+00 1.11e-01 6.45e+00 angle pdb=" C2 LMT A 301 " pdb=" C3 LMT A 301 " pdb=" C4 LMT A 301 " ideal model delta sigma weight residual 117.09 109.67 7.42 3.00e+00 1.11e-01 6.12e+00 angle pdb=" C6 LMT B 302 " pdb=" C7 LMT B 302 " pdb=" C8 LMT B 302 " ideal model delta sigma weight residual 117.26 110.14 7.12 3.00e+00 1.11e-01 5.64e+00 ... (remaining 4424 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 1707 17.88 - 35.76: 164 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 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: 0.260 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: 1.390 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 13.430 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 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 : 0.009 0.054 3278 Z= 0.574 Angle : 0.863 8.164 4429 Z= 0.404 Chirality : 0.046 0.146 497 Planarity : 0.003 0.029 526 Dihedral : 13.679 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 % Allowed : 0.00 % Favored : 100.00 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 24 HIS 0.002 0.001 HIS A 73 PHE 0.012 0.002 PHE A 31 TYR 0.012 0.002 TYR B 65 ARG 0.003 0.001 ARG A 165 *********************** 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 : 0.369 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 1.2616 time to fit residues: 77.7630 Evaluate side-chains 45 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.347 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4707 ------------------------------------------------------------------------------- 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: 0.9980 chunk 22 optimal weight: 0.1980 chunk 34 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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: 0.8456 moved from start: 0.1839 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= 0.194 Angle : 0.627 7.672 4429 Z= 0.323 Chirality : 0.041 0.136 497 Planarity : 0.004 0.028 526 Dihedral : 7.015 58.410 455 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.17 % Allowed : 11.08 % Favored : 87.76 % 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: 1.38 (0.44), residues: 375 helix: 1.66 (0.32), residues: 257 sheet: 0.23 (0.91), residues: 34 loop : -1.06 (0.71), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 133 HIS 0.002 0.001 HIS B 16 PHE 0.024 0.001 PHE A 29 TYR 0.010 0.002 TYR B 65 ARG 0.006 0.000 ARG A 143 *********************** 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: 4 poor density : 54 time to evaluate : 0.389 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 57 average time/residue: 1.0937 time to fit residues: 64.3058 Evaluate side-chains 47 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 46 time to evaluate : 0.310 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.4230 ------------------------------------------------------------------------------- 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: 1.9990 chunk 23 optimal weight: 0.0670 chunk 9 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 overall best weight: 0.7522 ------------------------------------------------------------------------------- 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: 0.8436 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3278 Z= 0.169 Angle : 0.562 9.150 4429 Z= 0.284 Chirality : 0.040 0.164 497 Planarity : 0.003 0.025 526 Dihedral : 5.835 54.589 455 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.04 % Allowed : 14.29 % Favored : 83.67 % 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: 1.82 (0.45), residues: 375 helix: 2.13 (0.33), residues: 253 sheet: 0.37 (0.92), residues: 34 loop : -1.23 (0.68), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 133 HIS 0.001 0.001 HIS A 67 PHE 0.028 0.001 PHE A 29 TYR 0.007 0.001 TYR B 158 ARG 0.004 0.000 ARG A 143 *********************** 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 59 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 52 time to evaluate : 0.377 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 56 average time/residue: 1.3179 time to fit residues: 76.0880 Evaluate side-chains 53 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 50 time to evaluate : 0.337 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 0.0307 time to fit residues: 0.5189 ------------------------------------------------------------------------------- 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: 0.7980 chunk 23 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 20 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 27 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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: 0.8473 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 3278 Z= 0.296 Angle : 0.613 8.448 4429 Z= 0.312 Chirality : 0.042 0.155 497 Planarity : 0.003 0.028 526 Dihedral : 5.794 50.212 455 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.17 % Allowed : 19.53 % Favored : 79.30 % 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: 1.90 (0.45), residues: 375 helix: 2.17 (0.33), residues: 253 sheet: 0.35 (0.93), residues: 34 loop : -1.11 (0.70), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 44 HIS 0.001 0.001 HIS A 73 PHE 0.013 0.001 PHE A 31 TYR 0.012 0.001 TYR B 65 ARG 0.002 0.000 ARG B 75 *********************** 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 55 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 51 time to evaluate : 0.377 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 54 average time/residue: 1.1733 time to fit residues: 65.2327 Evaluate side-chains 50 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 48 time to evaluate : 0.379 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.4878 ------------------------------------------------------------------------------- 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: 1.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 18 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 33 optimal weight: 0.0570 chunk 7 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 overall best weight: 0.9300 ------------------------------------------------------------------------------- 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: 0.8442 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3278 Z= 0.181 Angle : 0.577 8.662 4429 Z= 0.288 Chirality : 0.040 0.164 497 Planarity : 0.003 0.030 526 Dihedral : 5.328 46.251 455 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.04 % Allowed : 19.53 % Favored : 78.43 % 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: 2.00 (0.45), residues: 375 helix: 2.29 (0.33), residues: 253 sheet: 0.45 (0.95), residues: 34 loop : -1.24 (0.67), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 133 HIS 0.001 0.000 HIS A 100 PHE 0.018 0.001 PHE A 141 TYR 0.007 0.001 TYR B 65 ARG 0.002 0.000 ARG A 143 *********************** 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 61 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 54 time to evaluate : 0.378 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 60 average time/residue: 1.0917 time to fit residues: 67.6177 Evaluate side-chains 53 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 52 time to evaluate : 0.369 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.4885 ------------------------------------------------------------------------------- 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: 2.9990 chunk 36 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 8.9990 chunk 35 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 20 optimal weight: 20.0000 chunk 26 optimal weight: 0.5980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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: 0.8442 moved from start: 0.2779 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= 0.195 Angle : 0.592 9.215 4429 Z= 0.292 Chirality : 0.042 0.167 497 Planarity : 0.003 0.028 526 Dihedral : 5.047 40.943 455 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.04 % Allowed : 21.28 % Favored : 76.68 % 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: 2.29 (0.33), residues: 253 sheet: 0.84 (1.03), residues: 28 loop : -0.94 (0.66), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 133 HIS 0.002 0.001 HIS B 16 PHE 0.016 0.001 PHE A 141 TYR 0.008 0.001 TYR B 68 ARG 0.002 0.000 ARG A 143 *********************** 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: 7 poor density : 54 time to evaluate : 0.350 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 59 average time/residue: 1.0830 time to fit residues: 65.9970 Evaluate side-chains 55 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 52 time to evaluate : 0.371 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.4853 ------------------------------------------------------------------------------- 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: 9.9990 chunk 30 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 11 optimal weight: 5.9990 chunk 7 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.8431 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3278 Z= 0.175 Angle : 0.577 8.975 4429 Z= 0.289 Chirality : 0.042 0.178 497 Planarity : 0.003 0.030 526 Dihedral : 4.739 34.540 455 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.46 % Allowed : 22.74 % Favored : 75.80 % 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: 2.15 (0.45), residues: 375 helix: 2.31 (0.33), residues: 253 sheet: 0.88 (1.03), residues: 28 loop : -0.93 (0.66), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 133 HIS 0.001 0.001 HIS A 94 PHE 0.017 0.001 PHE A 141 TYR 0.007 0.001 TYR B 68 ARG 0.002 0.000 ARG A 143 *********************** 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 57 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 52 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 57 average time/residue: 1.1179 time to fit residues: 65.7356 Evaluate side-chains 55 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 52 time to evaluate : 0.342 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.4537 ------------------------------------------------------------------------------- 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: 2.9990 chunk 3 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 33 optimal weight: 0.0030 chunk 35 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 14 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 10 optimal weight: 10.0000 overall best weight: 0.6790 ------------------------------------------------------------------------------- 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: 0.8419 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3278 Z= 0.161 Angle : 0.578 7.817 4429 Z= 0.290 Chirality : 0.041 0.184 497 Planarity : 0.003 0.028 526 Dihedral : 4.406 27.276 455 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.46 % Allowed : 23.32 % Favored : 75.22 % 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 (0.45), residues: 375 helix: 2.35 (0.33), residues: 253 sheet: 0.99 (1.05), residues: 28 loop : -0.94 (0.65), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 133 HIS 0.001 0.000 HIS A 100 PHE 0.040 0.001 PHE A 29 TYR 0.006 0.001 TYR B 68 ARG 0.002 0.000 ARG A 143 *********************** 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 57 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 52 time to evaluate : 0.388 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 56 average time/residue: 1.0964 time to fit residues: 63.3577 Evaluate side-chains 50 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 48 time to evaluate : 0.345 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.4937 ------------------------------------------------------------------------------- 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: 0.9990 chunk 32 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 17 optimal weight: 0.2980 chunk 25 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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: 0.8415 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3278 Z= 0.168 Angle : 0.608 8.470 4429 Z= 0.305 Chirality : 0.041 0.196 497 Planarity : 0.003 0.030 526 Dihedral : 4.350 24.460 455 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.46 % Allowed : 23.62 % Favored : 74.93 % 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: 2.24 (0.45), residues: 375 helix: 2.46 (0.33), residues: 248 sheet: 1.00 (1.06), residues: 28 loop : -1.00 (0.62), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 24 HIS 0.002 0.001 HIS A 16 PHE 0.017 0.001 PHE A 141 TYR 0.009 0.001 TYR B 136 ARG 0.003 0.000 ARG A 32 *********************** 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 54 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 49 time to evaluate : 0.369 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 54 average time/residue: 1.0312 time to fit residues: 57.6048 Evaluate side-chains 51 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 49 time to evaluate : 0.372 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.4901 ------------------------------------------------------------------------------- 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: 0.3980 chunk 32 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 8 optimal weight: 0.0770 chunk 30 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 overall best weight: 0.6540 ------------------------------------------------------------------------------- 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: 0.8406 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 0.039 3278 Z= 0.160 Angle : 0.618 8.925 4429 Z= 0.304 Chirality : 0.042 0.197 497 Planarity : 0.003 0.029 526 Dihedral : 4.236 21.118 455 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.87 % Allowed : 23.91 % Favored : 75.22 % 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: 2.24 (0.44), residues: 375 helix: 2.51 (0.33), residues: 248 sheet: 1.06 (1.06), residues: 28 loop : -1.15 (0.59), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 133 HIS 0.001 0.000 HIS B 16 PHE 0.017 0.001 PHE A 141 TYR 0.006 0.001 TYR B 158 ARG 0.002 0.000 ARG A 32 ********************** 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 56 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 53 time to evaluate : 0.386 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 55 average time/residue: 1.1728 time to fit residues: 66.4990 Evaluate side-chains 52 residues out of total 343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 49 time to evaluate : 0.372 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 1.0154 time to fit residues: 1.5310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.214 > 50: distance: 6 - 29: 26.364 distance: 12 - 33: 28.859 distance: 15 - 21: 15.931 distance: 16 - 37: 14.526 distance: 21 - 22: 31.845 distance: 22 - 23: 12.740 distance: 22 - 25: 16.902 distance: 23 - 24: 22.233 distance: 23 - 29: 33.738 distance: 24 - 44: 21.305 distance: 25 - 26: 29.295 distance: 26 - 27: 33.099 distance: 26 - 28: 50.884 distance: 29 - 30: 38.924 distance: 30 - 31: 45.483 distance: 31 - 32: 33.578 distance: 31 - 33: 34.752 distance: 33 - 34: 34.112 distance: 34 - 35: 5.568 distance: 35 - 36: 34.756 distance: 35 - 37: 21.607 distance: 37 - 38: 17.263 distance: 38 - 39: 12.023 distance: 38 - 41: 10.208 distance: 39 - 40: 11.610 distance: 39 - 44: 15.350 distance: 41 - 42: 11.021 distance: 41 - 43: 11.530 distance: 44 - 45: 9.245 distance: 45 - 46: 12.886 distance: 45 - 48: 5.989 distance: 46 - 47: 10.349 distance: 46 - 52: 4.276 distance: 48 - 49: 4.253 distance: 49 - 50: 6.049 distance: 52 - 53: 8.975 distance: 53 - 54: 11.241 distance: 53 - 56: 21.091 distance: 54 - 55: 14.746 distance: 54 - 61: 13.786 distance: 56 - 57: 20.057 distance: 57 - 58: 8.644 distance: 58 - 59: 6.878 distance: 59 - 60: 19.807 distance: 61 - 62: 12.435 distance: 62 - 63: 28.118 distance: 62 - 65: 19.495 distance: 63 - 64: 14.199 distance: 63 - 71: 22.734 distance: 65 - 66: 12.080 distance: 66 - 67: 4.608 distance: 66 - 68: 5.007 distance: 67 - 69: 8.699 distance: 68 - 70: 8.579 distance: 69 - 70: 6.561 distance: 71 - 72: 7.778 distance: 72 - 73: 35.715 distance: 72 - 75: 8.881 distance: 73 - 74: 17.113 distance: 73 - 77: 35.416 distance: 75 - 76: 32.952 distance: 77 - 78: 11.246 distance: 78 - 79: 33.244 distance: 78 - 81: 25.215 distance: 79 - 80: 27.023 distance: 79 - 84: 29.398 distance: 81 - 82: 27.996 distance: 81 - 83: 16.623 distance: 85 - 86: 13.396 distance: 85 - 88: 42.434 distance: 86 - 87: 24.725 distance: 86 - 90: 21.268 distance: 87 - 111: 19.135 distance: 88 - 89: 30.707