Starting phenix.real_space_refine on Tue Feb 13 09:41:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qbi_13887/02_2024/7qbi_13887.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qbi_13887/02_2024/7qbi_13887.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qbi_13887/02_2024/7qbi_13887.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qbi_13887/02_2024/7qbi_13887.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qbi_13887/02_2024/7qbi_13887.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qbi_13887/02_2024/7qbi_13887.pdb" } resolution = 3.46 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= 0.002 sd= 0.093 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 20 5.16 5 C 3360 2.51 5 N 718 2.21 5 O 898 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 143": "OE1" <-> "OE2" Residue "A TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 143": "OE1" <-> "OE2" Residue "B TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 4996 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2140 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 8, 'TRANS': 289} Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 3, 'ASN:plan1': 4, 'HIS:plan': 1, 'PHE:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 98 Chain: "I" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 120 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 10} Chain: "K" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 120 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 10} Chain: "B" Number of atoms: 2140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2140 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 8, 'TRANS': 289} Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 3, 'ASN:plan1': 4, 'HIS:plan': 1, 'PHE:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 98 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 168 Unusual residues: {'NAG': 2, 'Y01': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'Y01': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'Y01': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 168 Unusual residues: {'NAG': 2, 'Y01': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.48, per 1000 atoms: 0.70 Number of scatterers: 4996 At special positions: 0 Unit cell: (75.9, 73.7, 94.6, 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 20 16.00 O 898 8.00 N 718 7.00 C 3360 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 25 " " NAG A 502 " - " ASN A 32 " " NAG B 501 " - " ASN B 32 " " NAG B 502 " - " ASN B 25 " Time building additional restraints: 1.86 Conformation dependent library (CDL) restraints added in 918.4 milliseconds 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1180 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 2 sheets defined 78.8% alpha, 0.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 9 through 13 Processing helix chain 'A' and resid 18 through 21 removed outlier: 3.827A pdb=" N GLN A 21 " --> pdb=" O ASN A 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 18 through 21' Processing helix chain 'A' and resid 38 through 73 Processing helix chain 'A' and resid 78 through 102 Processing helix chain 'A' and resid 108 through 114 Processing helix chain 'A' and resid 116 through 120 Processing helix chain 'A' and resid 121 through 154 removed outlier: 3.522A pdb=" N VAL A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL A 152 " --> pdb=" O PHE A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 195 removed outlier: 3.921A pdb=" N VAL A 191 " --> pdb=" O LYS A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 236 removed outlier: 3.678A pdb=" N ASN A 205 " --> pdb=" O ASP A 201 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA A 206 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ARG A 233 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU A 236 " --> pdb=" O SER A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 268 removed outlier: 3.581A pdb=" N ILE A 246 " --> pdb=" O ASP A 242 " (cutoff:3.500A) Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 273 through 275 No H-bonds generated for 'chain 'A' and resid 273 through 275' Processing helix chain 'A' and resid 276 through 301 removed outlier: 3.801A pdb=" N VAL A 280 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N LEU A 289 " --> pdb=" O ALA A 285 " (cutoff:3.500A) Proline residue: A 290 - end of helix Processing helix chain 'B' and resid 9 through 13 Processing helix chain 'B' and resid 18 through 21 removed outlier: 3.827A pdb=" N GLN B 21 " --> pdb=" O ASN B 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 18 through 21' Processing helix chain 'B' and resid 38 through 73 Processing helix chain 'B' and resid 78 through 102 Processing helix chain 'B' and resid 108 through 114 Processing helix chain 'B' and resid 116 through 120 Processing helix chain 'B' and resid 121 through 154 removed outlier: 3.522A pdb=" N VAL B 125 " --> pdb=" O SER B 121 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL B 152 " --> pdb=" O PHE B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 195 removed outlier: 3.921A pdb=" N VAL B 191 " --> pdb=" O LYS B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 236 removed outlier: 3.678A pdb=" N ASN B 205 " --> pdb=" O ASP B 201 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA B 206 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ARG B 233 " --> pdb=" O ALA B 229 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU B 236 " --> pdb=" O SER B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 268 removed outlier: 3.600A pdb=" N ILE B 246 " --> pdb=" O ASP B 242 " (cutoff:3.500A) Proline residue: B 258 - end of helix Processing helix chain 'B' and resid 273 through 275 No H-bonds generated for 'chain 'B' and resid 273 through 275' Processing helix chain 'B' and resid 276 through 301 removed outlier: 3.801A pdb=" N VAL B 280 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LEU B 289 " --> pdb=" O ALA B 285 " (cutoff:3.500A) Proline residue: B 290 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 24 Processing sheet with id=AA2, first strand: chain 'B' and resid 23 through 24 372 hydrogen bonds defined for protein. 1086 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.37 Time building geometry restraints manager: 1.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 734 1.31 - 1.44: 1298 1.44 - 1.57: 3052 1.57 - 1.69: 6 1.69 - 1.82: 36 Bond restraints: 5126 Sorted by residual: bond pdb=" C7 NAG B 502 " pdb=" N2 NAG B 502 " ideal model delta sigma weight residual 1.346 1.455 -0.109 2.00e-02 2.50e+03 2.98e+01 bond pdb=" C7 NAG A 502 " pdb=" N2 NAG A 502 " ideal model delta sigma weight residual 1.346 1.453 -0.107 2.00e-02 2.50e+03 2.85e+01 bond pdb=" C7 NAG A 501 " pdb=" N2 NAG A 501 " ideal model delta sigma weight residual 1.346 1.453 -0.107 2.00e-02 2.50e+03 2.84e+01 bond pdb=" C7 NAG B 501 " pdb=" N2 NAG B 501 " ideal model delta sigma weight residual 1.346 1.452 -0.106 2.00e-02 2.50e+03 2.82e+01 bond pdb=" C1 NAG B 501 " pdb=" O5 NAG B 501 " ideal model delta sigma weight residual 1.406 1.504 -0.098 2.00e-02 2.50e+03 2.42e+01 ... (remaining 5121 not shown) Histogram of bond angle deviations from ideal: 99.17 - 106.15: 154 106.15 - 113.14: 3021 113.14 - 120.12: 1952 120.12 - 127.10: 1921 127.10 - 134.08: 44 Bond angle restraints: 7092 Sorted by residual: angle pdb=" N PHE B 244 " pdb=" CA PHE B 244 " pdb=" C PHE B 244 " ideal model delta sigma weight residual 111.33 104.11 7.22 1.21e+00 6.83e-01 3.56e+01 angle pdb=" N PHE A 244 " pdb=" CA PHE A 244 " pdb=" C PHE A 244 " ideal model delta sigma weight residual 111.33 104.51 6.82 1.21e+00 6.83e-01 3.18e+01 angle pdb=" C SER A 104 " pdb=" CA SER A 104 " pdb=" CB SER A 104 " ideal model delta sigma weight residual 114.40 108.58 5.82 1.25e+00 6.40e-01 2.17e+01 angle pdb=" C SER B 104 " pdb=" CA SER B 104 " pdb=" CB SER B 104 " ideal model delta sigma weight residual 114.40 108.63 5.77 1.25e+00 6.40e-01 2.13e+01 angle pdb=" N TRP A 70 " pdb=" CA TRP A 70 " pdb=" C TRP A 70 " ideal model delta sigma weight residual 111.03 106.31 4.72 1.11e+00 8.12e-01 1.81e+01 ... (remaining 7087 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.62: 3413 23.62 - 47.23: 160 47.23 - 70.85: 29 70.85 - 94.47: 12 94.47 - 118.08: 4 Dihedral angle restraints: 3618 sinusoidal: 1792 harmonic: 1826 Sorted by residual: dihedral pdb=" CAR Y01 I 102 " pdb=" CAV Y01 I 102 " pdb=" CBC Y01 I 102 " pdb=" CAZ Y01 I 102 " ideal model delta sinusoidal sigma weight residual 55.40 -62.68 118.08 1 3.00e+01 1.11e-03 1.57e+01 dihedral pdb=" CAR Y01 K 102 " pdb=" CAV Y01 K 102 " pdb=" CBC Y01 K 102 " pdb=" CAZ Y01 K 102 " ideal model delta sinusoidal sigma weight residual 55.40 -60.15 115.55 1 3.00e+01 1.11e-03 1.53e+01 dihedral pdb=" CAZ Y01 I 102 " pdb=" CAV Y01 I 102 " pdb=" CBC Y01 I 102 " pdb=" OAW Y01 I 102 " ideal model delta sinusoidal sigma weight residual -174.31 -59.08 -115.23 1 3.00e+01 1.11e-03 1.52e+01 ... (remaining 3615 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 738 0.061 - 0.122: 156 0.122 - 0.183: 20 0.183 - 0.244: 8 0.244 - 0.305: 2 Chirality restraints: 924 Sorted by residual: chirality pdb=" CA LEU B 236 " pdb=" N LEU B 236 " pdb=" C LEU B 236 " pdb=" CB LEU B 236 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CA LEU A 236 " pdb=" N LEU A 236 " pdb=" C LEU A 236 " pdb=" CB LEU A 236 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CA PHE B 244 " pdb=" N PHE B 244 " pdb=" C PHE B 244 " pdb=" CB PHE B 244 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 921 not shown) Planarity restraints: 804 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 219 " 0.021 2.00e-02 2.50e+03 4.19e-02 1.76e+01 pdb=" C SER A 219 " -0.072 2.00e-02 2.50e+03 pdb=" O SER A 219 " 0.027 2.00e-02 2.50e+03 pdb=" N PHE A 220 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 219 " -0.020 2.00e-02 2.50e+03 4.01e-02 1.60e+01 pdb=" C SER B 219 " 0.069 2.00e-02 2.50e+03 pdb=" O SER B 219 " -0.026 2.00e-02 2.50e+03 pdb=" N PHE B 220 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 74 " -0.275 9.50e-02 1.11e+02 1.23e-01 9.48e+00 pdb=" NE ARG A 74 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG A 74 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 74 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 74 " -0.008 2.00e-02 2.50e+03 ... (remaining 801 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 903 2.77 - 3.30: 5100 3.30 - 3.83: 8016 3.83 - 4.37: 9430 4.37 - 4.90: 16177 Nonbonded interactions: 39626 Sorted by model distance: nonbonded pdb=" OE1 GLN B 51 " pdb=" OH TYR B 98 " model vdw 2.231 2.440 nonbonded pdb=" OE1 GLN A 51 " pdb=" OH TYR A 98 " model vdw 2.232 2.440 nonbonded pdb=" O ARG B 122 " pdb=" ND1 HIS B 126 " model vdw 2.296 2.520 nonbonded pdb=" O ARG A 122 " pdb=" ND1 HIS A 126 " model vdw 2.297 2.520 nonbonded pdb=" NH2 ARG A 74 " pdb=" O ALA B 298 " model vdw 2.330 2.520 ... (remaining 39621 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'I' selection = chain 'K' } 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: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.150 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 18.280 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 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 : 0.008 0.109 5126 Z= 0.532 Angle : 1.064 10.390 7092 Z= 0.600 Chirality : 0.053 0.305 924 Planarity : 0.009 0.123 800 Dihedral : 14.753 118.083 2438 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.31), residues: 614 helix: -0.82 (0.22), residues: 444 sheet: None (None), residues: 0 loop : -0.86 (0.48), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 70 HIS 0.003 0.001 HIS A 94 PHE 0.025 0.003 PHE B 171 TYR 0.026 0.003 TYR A 266 ARG 0.007 0.001 ARG A 74 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 0.556 Fit side-chains REVERT: A 120 ILE cc_start: 0.8098 (mm) cc_final: 0.7731 (mm) REVERT: B 120 ILE cc_start: 0.8135 (mm) cc_final: 0.7768 (mm) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.1521 time to fit residues: 22.7696 Evaluate side-chains 104 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 7.9990 chunk 45 optimal weight: 0.0010 chunk 25 optimal weight: 0.9980 chunk 15 optimal weight: 20.0000 chunk 30 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 54 optimal weight: 8.9990 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 2 HIS K 2 HIS ** B 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 5126 Z= 0.226 Angle : 0.615 7.008 7092 Z= 0.292 Chirality : 0.037 0.132 924 Planarity : 0.003 0.020 800 Dihedral : 10.284 88.871 1592 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.44 % Allowed : 8.30 % Favored : 91.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.33), residues: 614 helix: 1.49 (0.23), residues: 446 sheet: None (None), residues: 0 loop : -0.13 (0.49), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 1 HIS 0.003 0.001 HIS B 94 PHE 0.018 0.001 PHE A 171 TYR 0.009 0.001 TYR B 17 ARG 0.001 0.000 ARG B 74 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 112 time to evaluate : 0.517 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 112 average time/residue: 0.1502 time to fit residues: 22.1081 Evaluate side-chains 103 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 101 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain B residue 179 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 5126 Z= 0.351 Angle : 0.707 8.286 7092 Z= 0.323 Chirality : 0.040 0.148 924 Planarity : 0.003 0.027 800 Dihedral : 9.992 78.076 1592 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.18 % Allowed : 13.54 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.33), residues: 614 helix: 2.17 (0.24), residues: 434 sheet: None (None), residues: 0 loop : -0.56 (0.45), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 1 HIS 0.005 0.002 HIS B 94 PHE 0.020 0.002 PHE A 55 TYR 0.009 0.002 TYR A 106 ARG 0.001 0.000 ARG B 76 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 103 time to evaluate : 0.544 Fit side-chains REVERT: A 64 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.7984 (tt) REVERT: A 149 GLN cc_start: 0.8142 (tt0) cc_final: 0.7813 (tt0) REVERT: B 64 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8045 (tt) REVERT: B 70 TRP cc_start: 0.7462 (OUTLIER) cc_final: 0.7225 (m100) outliers start: 10 outliers final: 5 residues processed: 106 average time/residue: 0.1574 time to fit residues: 21.7411 Evaluate side-chains 110 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 102 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 70 TRP Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 184 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 54 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 15 optimal weight: 30.0000 chunk 48 optimal weight: 1.9990 chunk 32 optimal weight: 0.0570 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 5126 Z= 0.206 Angle : 0.597 7.854 7092 Z= 0.276 Chirality : 0.037 0.135 924 Planarity : 0.003 0.025 800 Dihedral : 8.619 58.661 1592 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.93 % Allowed : 15.07 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.69 (0.33), residues: 614 helix: 2.49 (0.24), residues: 446 sheet: None (None), residues: 0 loop : -0.17 (0.47), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 3 HIS 0.003 0.001 HIS B 94 PHE 0.013 0.001 PHE B 171 TYR 0.008 0.001 TYR A 128 ARG 0.000 0.000 ARG B 76 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 102 time to evaluate : 0.536 Fit side-chains REVERT: A 64 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8034 (tt) REVERT: A 106 TYR cc_start: 0.8653 (OUTLIER) cc_final: 0.7908 (m-80) REVERT: A 149 GLN cc_start: 0.8092 (tt0) cc_final: 0.7787 (tt0) REVERT: B 64 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8051 (tt) REVERT: B 106 TYR cc_start: 0.8648 (OUTLIER) cc_final: 0.7914 (m-80) outliers start: 18 outliers final: 6 residues processed: 110 average time/residue: 0.1528 time to fit residues: 22.0113 Evaluate side-chains 109 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 99 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 106 TYR Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 197 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 8.9990 chunk 43 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 5126 Z= 0.295 Angle : 0.648 8.074 7092 Z= 0.296 Chirality : 0.039 0.137 924 Planarity : 0.003 0.026 800 Dihedral : 8.691 59.803 1592 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.28 % Allowed : 18.34 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.34), residues: 614 helix: 2.39 (0.24), residues: 448 sheet: None (None), residues: 0 loop : -0.43 (0.48), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 1 HIS 0.003 0.001 HIS A 94 PHE 0.016 0.001 PHE A 55 TYR 0.007 0.001 TYR B 128 ARG 0.001 0.000 ARG B 58 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 98 time to evaluate : 0.541 Fit side-chains REVERT: A 64 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8135 (tp) REVERT: A 106 TYR cc_start: 0.8682 (OUTLIER) cc_final: 0.7871 (m-80) REVERT: B 54 MET cc_start: 0.8002 (OUTLIER) cc_final: 0.6614 (mpp) REVERT: B 64 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8215 (tp) REVERT: B 106 TYR cc_start: 0.8679 (OUTLIER) cc_final: 0.7975 (m-80) outliers start: 15 outliers final: 8 residues processed: 103 average time/residue: 0.1560 time to fit residues: 21.0097 Evaluate side-chains 111 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 98 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 70 TRP Chi-restraints excluded: chain A residue 106 TYR Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 54 MET Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 197 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 19 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 5126 Z= 0.241 Angle : 0.593 6.804 7092 Z= 0.275 Chirality : 0.038 0.135 924 Planarity : 0.003 0.025 800 Dihedral : 8.462 59.815 1592 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.93 % Allowed : 19.00 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.84 (0.33), residues: 614 helix: 2.76 (0.24), residues: 434 sheet: None (None), residues: 0 loop : -0.39 (0.46), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 3 HIS 0.003 0.001 HIS A 94 PHE 0.012 0.001 PHE A 55 TYR 0.008 0.001 TYR A 128 ARG 0.000 0.000 ARG B 58 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 99 time to evaluate : 0.561 Fit side-chains REVERT: A 64 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8027 (tt) REVERT: A 106 TYR cc_start: 0.8683 (OUTLIER) cc_final: 0.7921 (m-80) REVERT: B 54 MET cc_start: 0.8044 (OUTLIER) cc_final: 0.6596 (mpp) REVERT: B 64 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8136 (tp) REVERT: B 106 TYR cc_start: 0.8686 (OUTLIER) cc_final: 0.7937 (m-80) outliers start: 18 outliers final: 10 residues processed: 107 average time/residue: 0.1596 time to fit residues: 22.2911 Evaluate side-chains 114 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 99 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 70 TRP Chi-restraints excluded: chain A residue 106 TYR Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 54 MET Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 197 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5126 Z= 0.226 Angle : 0.585 6.795 7092 Z= 0.273 Chirality : 0.038 0.132 924 Planarity : 0.003 0.025 800 Dihedral : 8.420 58.668 1592 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.93 % Allowed : 20.31 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.80 (0.34), residues: 614 helix: 2.59 (0.24), residues: 448 sheet: None (None), residues: 0 loop : -0.25 (0.49), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 3 HIS 0.003 0.001 HIS A 94 PHE 0.012 0.001 PHE A 55 TYR 0.008 0.001 TYR B 128 ARG 0.000 0.000 ARG A 122 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 100 time to evaluate : 0.485 Fit side-chains REVERT: A 64 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8005 (tt) REVERT: A 106 TYR cc_start: 0.8675 (OUTLIER) cc_final: 0.7971 (m-80) REVERT: B 54 MET cc_start: 0.8049 (OUTLIER) cc_final: 0.6601 (mpp) REVERT: B 64 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8124 (tp) REVERT: B 106 TYR cc_start: 0.8684 (OUTLIER) cc_final: 0.7988 (m-80) outliers start: 18 outliers final: 10 residues processed: 107 average time/residue: 0.1453 time to fit residues: 20.3747 Evaluate side-chains 114 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 99 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 70 TRP Chi-restraints excluded: chain A residue 106 TYR Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 54 MET Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 197 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 23 optimal weight: 8.9990 chunk 42 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5126 Z= 0.249 Angle : 0.599 7.160 7092 Z= 0.279 Chirality : 0.038 0.135 924 Planarity : 0.003 0.026 800 Dihedral : 8.650 59.729 1592 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.93 % Allowed : 20.31 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.85 (0.34), residues: 614 helix: 2.61 (0.23), residues: 448 sheet: None (None), residues: 0 loop : -0.18 (0.50), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 3 HIS 0.003 0.001 HIS A 94 PHE 0.015 0.001 PHE A 55 TYR 0.007 0.001 TYR A 17 ARG 0.001 0.000 ARG B 58 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 104 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8089 (tp) REVERT: A 106 TYR cc_start: 0.8674 (OUTLIER) cc_final: 0.7977 (m-80) REVERT: B 54 MET cc_start: 0.8026 (OUTLIER) cc_final: 0.6525 (mpp) REVERT: B 64 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8141 (tp) REVERT: B 106 TYR cc_start: 0.8661 (OUTLIER) cc_final: 0.7888 (m-80) outliers start: 18 outliers final: 12 residues processed: 111 average time/residue: 0.1534 time to fit residues: 22.3306 Evaluate side-chains 118 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 101 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 70 TRP Chi-restraints excluded: chain A residue 106 TYR Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 54 MET Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 70 TRP Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 197 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 chunk 59 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5126 Z= 0.217 Angle : 0.570 6.559 7092 Z= 0.270 Chirality : 0.037 0.137 924 Planarity : 0.003 0.026 800 Dihedral : 8.500 58.152 1592 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.49 % Allowed : 21.18 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.02 (0.34), residues: 614 helix: 2.76 (0.23), residues: 448 sheet: None (None), residues: 0 loop : -0.18 (0.50), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 3 HIS 0.002 0.001 HIS B 94 PHE 0.011 0.001 PHE A 55 TYR 0.007 0.001 TYR B 128 ARG 0.004 0.000 ARG A 74 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 104 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8027 (tt) REVERT: A 106 TYR cc_start: 0.8638 (OUTLIER) cc_final: 0.7843 (m-80) REVERT: B 64 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8153 (tp) REVERT: B 106 TYR cc_start: 0.8631 (OUTLIER) cc_final: 0.7789 (m-80) outliers start: 16 outliers final: 11 residues processed: 111 average time/residue: 0.1500 time to fit residues: 21.8346 Evaluate side-chains 118 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 103 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 70 TRP Chi-restraints excluded: chain A residue 106 TYR Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 197 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 50 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 7 optimal weight: 0.3980 chunk 13 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5126 Z= 0.203 Angle : 0.563 6.460 7092 Z= 0.269 Chirality : 0.037 0.135 924 Planarity : 0.003 0.026 800 Dihedral : 8.348 56.901 1592 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.84 % Allowed : 22.93 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.11 (0.34), residues: 614 helix: 2.82 (0.23), residues: 448 sheet: None (None), residues: 0 loop : -0.14 (0.50), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 3 HIS 0.002 0.001 HIS A 94 PHE 0.011 0.001 PHE A 55 TYR 0.007 0.001 TYR B 128 ARG 0.000 0.000 ARG A 76 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 103 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.7985 (tt) REVERT: B 54 MET cc_start: 0.8057 (OUTLIER) cc_final: 0.6624 (mpp) REVERT: B 64 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8123 (tt) outliers start: 13 outliers final: 10 residues processed: 108 average time/residue: 0.1570 time to fit residues: 22.3375 Evaluate side-chains 115 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 102 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 70 TRP Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 54 MET Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 70 TRP Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 197 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 0.2980 chunk 6 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 8.9990 chunk 32 optimal weight: 0.0000 chunk 40 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.180303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.139685 restraints weight = 6542.150| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.47 r_work: 0.3449 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5126 Z= 0.193 Angle : 0.554 6.415 7092 Z= 0.267 Chirality : 0.037 0.137 924 Planarity : 0.003 0.027 800 Dihedral : 8.143 55.925 1592 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.84 % Allowed : 22.49 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.19 (0.34), residues: 614 helix: 2.88 (0.23), residues: 448 sheet: None (None), residues: 0 loop : -0.12 (0.50), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 3 HIS 0.002 0.001 HIS A 94 PHE 0.010 0.001 PHE A 55 TYR 0.007 0.001 TYR A 128 ARG 0.001 0.000 ARG B 76 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1244.81 seconds wall clock time: 23 minutes 21.33 seconds (1401.33 seconds total)