Starting phenix.real_space_refine on Wed Jan 17 15:32:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nt6_0503/01_2024/6nt6_0503.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nt6_0503/01_2024/6nt6_0503.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nt6_0503/01_2024/6nt6_0503.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nt6_0503/01_2024/6nt6_0503.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nt6_0503/01_2024/6nt6_0503.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nt6_0503/01_2024/6nt6_0503.pdb" } resolution = 4.0 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= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 2712 2.51 5 N 724 2.21 5 O 726 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 20": "NH1" <-> "NH2" Residue "A PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 20": "NH1" <-> "NH2" Residue "B PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 4198 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2099 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 10, 'TRANS': 267} Chain breaks: 7 Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 160 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 3, 'TRP:plan': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 95 Chain: "B" Number of atoms: 2099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2099 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 10, 'TRANS': 267} Chain breaks: 7 Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 160 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 3, 'TRP:plan': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 95 Time building chain proxies: 2.82, per 1000 atoms: 0.67 Number of scatterers: 4198 At special positions: 0 Unit cell: (88.2, 61.32, 98.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 726 8.00 N 724 7.00 C 2712 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.55 Conformation dependent library (CDL) restraints added in 710.4 milliseconds 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1064 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 2 sheets defined 67.3% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 23 through 41 Processing helix chain 'A' and resid 48 through 75 removed outlier: 3.802A pdb=" N SER A 52 " --> pdb=" O PRO A 48 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLY A 63 " --> pdb=" O ALA A 59 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N VAL A 64 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU A 65 " --> pdb=" O GLN A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 83 Processing helix chain 'A' and resid 88 through 95 removed outlier: 4.129A pdb=" N PHE A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 111 removed outlier: 4.579A pdb=" N ALA A 102 " --> pdb=" O ARG A 98 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LEU A 103 " --> pdb=" O TRP A 99 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU A 104 " --> pdb=" O TYR A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 140 removed outlier: 3.715A pdb=" N LEU A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 156 removed outlier: 3.553A pdb=" N SER A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 171 removed outlier: 4.344A pdb=" N GLY A 163 " --> pdb=" O ASN A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 188 Proline residue: A 178 - end of helix removed outlier: 4.432A pdb=" N LYS A 181 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 221 Processing helix chain 'A' and resid 269 through 279 removed outlier: 4.008A pdb=" N SER A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN A 278 " --> pdb=" O CYS A 274 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP A 279 " --> pdb=" O ALA A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 306 removed outlier: 3.697A pdb=" N SER A 306 " --> pdb=" O ASP A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 346 removed outlier: 3.794A pdb=" N ILE A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 41 Processing helix chain 'B' and resid 48 through 75 removed outlier: 3.802A pdb=" N SER B 52 " --> pdb=" O PRO B 48 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLY B 63 " --> pdb=" O ALA B 59 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N VAL B 64 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU B 65 " --> pdb=" O GLN B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 83 Processing helix chain 'B' and resid 88 through 95 removed outlier: 4.129A pdb=" N PHE B 95 " --> pdb=" O LEU B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 111 removed outlier: 4.580A pdb=" N ALA B 102 " --> pdb=" O ARG B 98 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LEU B 103 " --> pdb=" O TRP B 99 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU B 104 " --> pdb=" O TYR B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 140 removed outlier: 3.716A pdb=" N LEU B 139 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY B 140 " --> pdb=" O VAL B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 156 removed outlier: 3.553A pdb=" N SER B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 171 removed outlier: 4.344A pdb=" N GLY B 163 " --> pdb=" O ASN B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 188 Proline residue: B 178 - end of helix removed outlier: 4.432A pdb=" N LYS B 181 " --> pdb=" O LEU B 177 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLU B 182 " --> pdb=" O PRO B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 221 Processing helix chain 'B' and resid 269 through 279 removed outlier: 4.007A pdb=" N SER B 277 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN B 278 " --> pdb=" O CYS B 274 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP B 279 " --> pdb=" O ALA B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 306 removed outlier: 3.697A pdb=" N SER B 306 " --> pdb=" O ASP B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 346 removed outlier: 3.793A pdb=" N ILE B 334 " --> pdb=" O LEU B 330 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 224 through 226 removed outlier: 4.469A pdb=" N SER A 248 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU A 264 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE A 205 " --> pdb=" O ARG A 315 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 224 through 226 removed outlier: 4.470A pdb=" N SER B 248 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU B 264 " --> pdb=" O SER B 248 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE B 205 " --> pdb=" O ARG B 315 " (cutoff:3.500A) 252 hydrogen bonds defined for protein. 750 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: 1.06 Time building geometry restraints manager: 1.72 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: 1336 1.34 - 1.46: 730 1.46 - 1.58: 2164 1.58 - 1.69: 0 1.69 - 1.81: 40 Bond restraints: 4270 Sorted by residual: bond pdb=" CA ALA A 47 " pdb=" C ALA A 47 " ideal model delta sigma weight residual 1.525 1.560 -0.035 2.10e-02 2.27e+03 2.74e+00 bond pdb=" CA ALA B 47 " pdb=" C ALA B 47 " ideal model delta sigma weight residual 1.525 1.559 -0.034 2.10e-02 2.27e+03 2.67e+00 bond pdb=" CG PRO B 269 " pdb=" CD PRO B 269 " ideal model delta sigma weight residual 1.503 1.465 0.038 3.40e-02 8.65e+02 1.27e+00 bond pdb=" CG PRO A 269 " pdb=" CD PRO A 269 " ideal model delta sigma weight residual 1.503 1.465 0.038 3.40e-02 8.65e+02 1.27e+00 bond pdb=" CA LEU A 177 " pdb=" C LEU A 177 " ideal model delta sigma weight residual 1.522 1.536 -0.014 1.26e-02 6.30e+03 1.19e+00 ... (remaining 4265 not shown) Histogram of bond angle deviations from ideal: 100.16 - 106.92: 118 106.92 - 113.68: 2518 113.68 - 120.44: 1621 120.44 - 127.20: 1487 127.20 - 133.96: 48 Bond angle restraints: 5792 Sorted by residual: angle pdb=" N LEU A 177 " pdb=" CA LEU A 177 " pdb=" C LEU A 177 " ideal model delta sigma weight residual 113.16 117.31 -4.15 1.42e+00 4.96e-01 8.53e+00 angle pdb=" N LEU B 177 " pdb=" CA LEU B 177 " pdb=" C LEU B 177 " ideal model delta sigma weight residual 113.16 117.30 -4.14 1.42e+00 4.96e-01 8.52e+00 angle pdb=" CA ALA A 47 " pdb=" C ALA A 47 " pdb=" N PRO A 48 " ideal model delta sigma weight residual 116.90 121.25 -4.35 1.50e+00 4.44e-01 8.39e+00 angle pdb=" CA ALA B 47 " pdb=" C ALA B 47 " pdb=" N PRO B 48 " ideal model delta sigma weight residual 116.90 121.24 -4.34 1.50e+00 4.44e-01 8.37e+00 angle pdb=" CA LEU A 217 " pdb=" CB LEU A 217 " pdb=" CG LEU A 217 " ideal model delta sigma weight residual 116.30 106.45 9.85 3.50e+00 8.16e-02 7.92e+00 ... (remaining 5787 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.10: 2278 14.10 - 28.19: 242 28.19 - 42.29: 34 42.29 - 56.39: 6 56.39 - 70.49: 4 Dihedral angle restraints: 2564 sinusoidal: 942 harmonic: 1622 Sorted by residual: dihedral pdb=" CA SER B 268 " pdb=" C SER B 268 " pdb=" N PRO B 269 " pdb=" CA PRO B 269 " ideal model delta harmonic sigma weight residual 180.00 -159.70 -20.30 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA SER A 268 " pdb=" C SER A 268 " pdb=" N PRO A 269 " pdb=" CA PRO A 269 " ideal model delta harmonic sigma weight residual -180.00 -159.73 -20.27 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA ILE A 76 " pdb=" C ILE A 76 " pdb=" N PHE A 77 " pdb=" CA PHE A 77 " ideal model delta harmonic sigma weight residual -180.00 -162.21 -17.79 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 2561 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 416 0.032 - 0.063: 199 0.063 - 0.095: 59 0.095 - 0.127: 26 0.127 - 0.158: 4 Chirality restraints: 704 Sorted by residual: chirality pdb=" CA LEU B 177 " pdb=" N LEU B 177 " pdb=" C LEU B 177 " pdb=" CB LEU B 177 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.27e-01 chirality pdb=" CA LEU A 177 " pdb=" N LEU A 177 " pdb=" C LEU A 177 " pdb=" CB LEU A 177 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.05e-01 chirality pdb=" CA SER B 268 " pdb=" N SER B 268 " pdb=" C SER B 268 " pdb=" CB SER B 268 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.76e-01 ... (remaining 701 not shown) Planarity restraints: 712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 95 " 0.036 5.00e-02 4.00e+02 5.38e-02 4.63e+00 pdb=" N PRO A 96 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 96 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 96 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 95 " 0.036 5.00e-02 4.00e+02 5.38e-02 4.63e+00 pdb=" N PRO B 96 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 96 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 96 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 18 " 0.034 5.00e-02 4.00e+02 5.11e-02 4.18e+00 pdb=" N PRO B 19 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO B 19 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 19 " 0.028 5.00e-02 4.00e+02 ... (remaining 709 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 1309 2.83 - 3.35: 3693 3.35 - 3.87: 6331 3.87 - 4.38: 6712 4.38 - 4.90: 11611 Nonbonded interactions: 29656 Sorted by model distance: nonbonded pdb=" OH TYR B 172 " pdb=" OE2 GLU B 265 " model vdw 2.316 2.440 nonbonded pdb=" OH TYR A 172 " pdb=" OE2 GLU A 265 " model vdw 2.316 2.440 nonbonded pdb=" O LEU B 126 " pdb=" OG SER B 129 " model vdw 2.327 2.440 nonbonded pdb=" O LEU A 126 " pdb=" OG SER A 129 " model vdw 2.327 2.440 nonbonded pdb=" OH TYR A 169 " pdb=" NZ LYS A 174 " model vdw 2.332 2.520 ... (remaining 29651 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.210 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: 1.180 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 16.270 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 4270 Z= 0.319 Angle : 0.795 9.850 5792 Z= 0.424 Chirality : 0.043 0.158 704 Planarity : 0.007 0.054 712 Dihedral : 11.988 70.486 1500 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % 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: -3.32 (0.29), residues: 524 helix: -1.69 (0.22), residues: 330 sheet: -1.62 (0.63), residues: 56 loop : -3.30 (0.37), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 99 HIS 0.005 0.001 HIS B 204 PHE 0.019 0.003 PHE A 95 TYR 0.008 0.002 TYR A 319 ARG 0.004 0.001 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 LEU cc_start: 0.8032 (mt) cc_final: 0.7717 (tp) REVERT: A 148 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7831 (mt-10) REVERT: A 158 LYS cc_start: 0.8768 (mtmt) cc_final: 0.8499 (mttp) REVERT: A 183 CYS cc_start: 0.8369 (m) cc_final: 0.8093 (m) REVERT: A 302 ASP cc_start: 0.8483 (m-30) cc_final: 0.8239 (m-30) REVERT: A 310 CYS cc_start: 0.8755 (m) cc_final: 0.8286 (m) REVERT: B 105 LEU cc_start: 0.8034 (mt) cc_final: 0.7701 (tp) REVERT: B 132 CYS cc_start: 0.7914 (m) cc_final: 0.7644 (m) REVERT: B 148 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7694 (mt-10) REVERT: B 151 GLU cc_start: 0.8732 (tt0) cc_final: 0.8502 (tm-30) REVERT: B 158 LYS cc_start: 0.8718 (mtmt) cc_final: 0.8430 (mttp) REVERT: B 183 CYS cc_start: 0.8395 (m) cc_final: 0.8120 (m) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.1508 time to fit residues: 27.9791 Evaluate side-chains 72 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 8.9990 chunk 40 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 13 optimal weight: 0.5980 chunk 27 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 42 optimal weight: 20.0000 chunk 16 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 49 optimal weight: 0.1980 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 HIS ** B 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4270 Z= 0.228 Angle : 0.684 8.499 5792 Z= 0.325 Chirality : 0.039 0.142 704 Planarity : 0.005 0.038 712 Dihedral : 4.878 15.013 586 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.53 % Allowed : 16.36 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.35), residues: 524 helix: 0.66 (0.28), residues: 318 sheet: -1.71 (0.63), residues: 56 loop : -2.54 (0.42), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 99 HIS 0.005 0.001 HIS A 204 PHE 0.011 0.002 PHE A 95 TYR 0.005 0.001 TYR B 169 ARG 0.002 0.000 ARG A 301 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 83 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 LEU cc_start: 0.8143 (mt) cc_final: 0.7804 (tp) REVERT: A 276 MET cc_start: 0.8307 (mtm) cc_final: 0.7886 (ttm) REVERT: B 70 CYS cc_start: 0.8657 (m) cc_final: 0.8255 (t) REVERT: B 105 LEU cc_start: 0.8036 (mt) cc_final: 0.7698 (tp) REVERT: B 148 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7796 (mt-10) REVERT: B 158 LYS cc_start: 0.8636 (mtmt) cc_final: 0.8434 (mttp) REVERT: B 276 MET cc_start: 0.8258 (mtm) cc_final: 0.7901 (ttm) outliers start: 11 outliers final: 7 residues processed: 92 average time/residue: 0.1516 time to fit residues: 18.0658 Evaluate side-chains 67 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 60 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 66 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 0.0370 chunk 15 optimal weight: 30.0000 chunk 40 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 chunk 13 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 9.9990 chunk 43 optimal weight: 9.9990 chunk 48 optimal weight: 0.6980 chunk 16 optimal weight: 9.9990 chunk 39 optimal weight: 8.9990 overall best weight: 1.7062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4270 Z= 0.178 Angle : 0.622 7.940 5792 Z= 0.296 Chirality : 0.039 0.168 704 Planarity : 0.004 0.032 712 Dihedral : 4.635 20.523 586 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.84 % Allowed : 18.89 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.37), residues: 524 helix: 1.47 (0.29), residues: 322 sheet: -1.69 (0.65), residues: 56 loop : -2.38 (0.43), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 336 HIS 0.004 0.001 HIS A 337 PHE 0.005 0.001 PHE B 36 TYR 0.020 0.001 TYR B 319 ARG 0.002 0.000 ARG B 98 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 84 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 LEU cc_start: 0.8100 (mt) cc_final: 0.7787 (tp) REVERT: A 133 GLN cc_start: 0.8923 (mm-40) cc_final: 0.8584 (mt0) REVERT: B 105 LEU cc_start: 0.8101 (mt) cc_final: 0.7766 (tp) outliers start: 8 outliers final: 3 residues processed: 91 average time/residue: 0.1320 time to fit residues: 15.8860 Evaluate side-chains 68 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 65 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain B residue 39 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 0.0370 chunk 36 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 52 optimal weight: 0.1980 chunk 46 optimal weight: 20.0000 chunk 14 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 overall best weight: 1.6464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4270 Z= 0.172 Angle : 0.599 7.067 5792 Z= 0.281 Chirality : 0.037 0.141 704 Planarity : 0.004 0.033 712 Dihedral : 4.531 25.233 586 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.23 % Allowed : 17.74 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.37), residues: 524 helix: 1.83 (0.29), residues: 326 sheet: -1.57 (0.67), residues: 56 loop : -2.27 (0.43), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 99 HIS 0.003 0.000 HIS B 204 PHE 0.022 0.001 PHE A 95 TYR 0.008 0.001 TYR A 314 ARG 0.001 0.000 ARG B 98 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 73 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 LEU cc_start: 0.8103 (mt) cc_final: 0.7775 (tp) REVERT: A 308 LYS cc_start: 0.8812 (mmmt) cc_final: 0.8446 (mttt) REVERT: A 319 TYR cc_start: 0.9003 (p90) cc_final: 0.8688 (p90) REVERT: B 105 LEU cc_start: 0.8120 (mt) cc_final: 0.7805 (tp) outliers start: 14 outliers final: 6 residues processed: 85 average time/residue: 0.1270 time to fit residues: 14.3445 Evaluate side-chains 67 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 61 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 272 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 21 optimal weight: 0.3980 chunk 44 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 chunk 13 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 HIS ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4270 Z= 0.244 Angle : 0.630 6.767 5792 Z= 0.302 Chirality : 0.038 0.139 704 Planarity : 0.004 0.031 712 Dihedral : 4.578 20.603 586 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 4.15 % Allowed : 21.43 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.37), residues: 524 helix: 2.02 (0.29), residues: 324 sheet: -1.55 (0.70), residues: 56 loop : -2.27 (0.42), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 99 HIS 0.003 0.001 HIS A 247 PHE 0.029 0.002 PHE A 95 TYR 0.019 0.002 TYR B 319 ARG 0.003 0.000 ARG B 98 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 63 time to evaluate : 0.600 Fit side-chains REVERT: A 105 LEU cc_start: 0.8124 (mt) cc_final: 0.7786 (tp) REVERT: A 319 TYR cc_start: 0.9058 (p90) cc_final: 0.8811 (p90) REVERT: B 105 LEU cc_start: 0.8058 (mt) cc_final: 0.7722 (tp) REVERT: B 276 MET cc_start: 0.8077 (ttm) cc_final: 0.7870 (tmm) outliers start: 18 outliers final: 9 residues processed: 77 average time/residue: 0.1307 time to fit residues: 13.6985 Evaluate side-chains 66 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 57 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 303 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 3.9990 chunk 30 optimal weight: 8.9990 chunk 12 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 17 optimal weight: 0.0770 chunk 27 optimal weight: 20.0000 chunk 50 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 overall best weight: 1.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4270 Z= 0.163 Angle : 0.605 6.428 5792 Z= 0.286 Chirality : 0.037 0.139 704 Planarity : 0.004 0.032 712 Dihedral : 4.396 18.717 586 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.23 % Allowed : 22.58 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.38), residues: 524 helix: 2.14 (0.29), residues: 326 sheet: -1.74 (0.70), residues: 60 loop : -1.99 (0.46), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 99 HIS 0.003 0.000 HIS A 337 PHE 0.027 0.001 PHE A 95 TYR 0.009 0.001 TYR A 314 ARG 0.001 0.000 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 70 time to evaluate : 0.496 Fit side-chains REVERT: A 105 LEU cc_start: 0.8101 (mt) cc_final: 0.7754 (tp) REVERT: A 159 ASN cc_start: 0.8400 (m-40) cc_final: 0.8182 (t0) REVERT: A 266 PHE cc_start: 0.8843 (OUTLIER) cc_final: 0.8152 (m-10) REVERT: A 308 LYS cc_start: 0.8763 (mmmt) cc_final: 0.8493 (mttt) REVERT: A 319 TYR cc_start: 0.9018 (p90) cc_final: 0.8812 (p90) REVERT: B 105 LEU cc_start: 0.8105 (mt) cc_final: 0.7783 (tp) outliers start: 14 outliers final: 5 residues processed: 80 average time/residue: 0.1217 time to fit residues: 13.2902 Evaluate side-chains 68 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 62 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain B residue 39 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 9.9990 chunk 38 optimal weight: 8.9990 chunk 43 optimal weight: 0.9990 chunk 52 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 24 optimal weight: 0.0370 chunk 20 optimal weight: 0.0060 chunk 15 optimal weight: 0.0010 chunk 10 optimal weight: 0.6980 chunk 33 optimal weight: 8.9990 overall best weight: 0.3482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.4121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 4270 Z= 0.159 Angle : 0.617 7.162 5792 Z= 0.286 Chirality : 0.037 0.144 704 Planarity : 0.004 0.034 712 Dihedral : 4.279 23.215 586 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.38 % Allowed : 24.42 % Favored : 74.19 % 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: 1.13 (0.38), residues: 524 helix: 2.26 (0.29), residues: 326 sheet: -1.58 (0.71), residues: 60 loop : -1.92 (0.45), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 99 HIS 0.003 0.000 HIS A 337 PHE 0.023 0.001 PHE A 95 TYR 0.017 0.001 TYR B 319 ARG 0.001 0.000 ARG A 51 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 74 time to evaluate : 0.541 Fit side-chains revert: symmetry clash REVERT: A 105 LEU cc_start: 0.8104 (mt) cc_final: 0.7766 (tp) REVERT: A 159 ASN cc_start: 0.8413 (m-40) cc_final: 0.8101 (t0) REVERT: A 266 PHE cc_start: 0.8730 (OUTLIER) cc_final: 0.8083 (m-10) REVERT: A 291 GLU cc_start: 0.8596 (mm-30) cc_final: 0.8304 (pt0) REVERT: A 308 LYS cc_start: 0.8831 (mmmt) cc_final: 0.8506 (mttt) REVERT: A 319 TYR cc_start: 0.8943 (p90) cc_final: 0.8733 (p90) REVERT: B 105 LEU cc_start: 0.8134 (mt) cc_final: 0.7817 (tp) outliers start: 6 outliers final: 3 residues processed: 79 average time/residue: 0.1104 time to fit residues: 12.1696 Evaluate side-chains 67 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 63 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain B residue 271 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 7.9990 chunk 25 optimal weight: 9.9990 chunk 4 optimal weight: 7.9990 chunk 40 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 45 optimal weight: 9.9990 chunk 48 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 chunk 21 optimal weight: 0.0370 chunk 38 optimal weight: 2.9990 overall best weight: 2.5864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 GLN ** B 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.4227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4270 Z= 0.197 Angle : 0.627 9.023 5792 Z= 0.293 Chirality : 0.037 0.130 704 Planarity : 0.004 0.034 712 Dihedral : 4.285 22.855 586 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.53 % Allowed : 25.35 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.38), residues: 524 helix: 2.42 (0.29), residues: 326 sheet: -1.52 (0.72), residues: 60 loop : -1.87 (0.45), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 166 HIS 0.002 0.001 HIS A 337 PHE 0.023 0.001 PHE A 95 TYR 0.009 0.001 TYR A 314 ARG 0.003 0.000 ARG B 315 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 62 time to evaluate : 0.524 Fit side-chains revert: symmetry clash REVERT: A 105 LEU cc_start: 0.8176 (mt) cc_final: 0.7835 (tp) REVERT: A 159 ASN cc_start: 0.8367 (m-40) cc_final: 0.8122 (t0) REVERT: A 266 PHE cc_start: 0.8803 (OUTLIER) cc_final: 0.8099 (m-10) REVERT: A 291 GLU cc_start: 0.8630 (mm-30) cc_final: 0.8318 (pt0) REVERT: A 308 LYS cc_start: 0.8829 (mmmt) cc_final: 0.8559 (mttt) REVERT: A 319 TYR cc_start: 0.8997 (p90) cc_final: 0.8761 (p90) REVERT: B 70 CYS cc_start: 0.8709 (m) cc_final: 0.8435 (t) REVERT: B 105 LEU cc_start: 0.8217 (mt) cc_final: 0.7879 (tp) outliers start: 11 outliers final: 5 residues processed: 70 average time/residue: 0.1167 time to fit residues: 11.3642 Evaluate side-chains 64 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 58 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain B residue 130 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 45 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 24 optimal weight: 8.9990 chunk 35 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 49 optimal weight: 0.0170 chunk 42 optimal weight: 10.0000 overall best weight: 0.7420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.4368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 4270 Z= 0.141 Angle : 0.624 9.386 5792 Z= 0.284 Chirality : 0.037 0.156 704 Planarity : 0.004 0.033 712 Dihedral : 4.092 23.101 586 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.84 % Allowed : 25.35 % Favored : 72.81 % 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: 1.43 (0.38), residues: 524 helix: 2.50 (0.29), residues: 326 sheet: -1.47 (0.71), residues: 60 loop : -1.84 (0.46), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 99 HIS 0.002 0.000 HIS A 337 PHE 0.020 0.001 PHE A 95 TYR 0.019 0.001 TYR B 319 ARG 0.002 0.000 ARG B 315 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 65 time to evaluate : 0.535 Fit side-chains revert: symmetry clash REVERT: A 105 LEU cc_start: 0.8085 (mt) cc_final: 0.7749 (tp) REVERT: A 159 ASN cc_start: 0.8326 (m-40) cc_final: 0.7929 (t0) REVERT: A 266 PHE cc_start: 0.8622 (OUTLIER) cc_final: 0.7839 (m-10) REVERT: A 291 GLU cc_start: 0.8600 (mm-30) cc_final: 0.8312 (pt0) REVERT: A 308 LYS cc_start: 0.8864 (mmmt) cc_final: 0.8509 (mttt) REVERT: B 105 LEU cc_start: 0.8225 (mt) cc_final: 0.7917 (tp) outliers start: 8 outliers final: 4 residues processed: 73 average time/residue: 0.1037 time to fit residues: 10.8113 Evaluate side-chains 66 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 61 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain B residue 271 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 34 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 13 optimal weight: 8.9990 chunk 39 optimal weight: 8.9990 chunk 6 optimal weight: 0.0970 chunk 11 optimal weight: 6.9990 chunk 42 optimal weight: 20.0000 chunk 17 optimal weight: 2.9990 overall best weight: 3.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.4368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4270 Z= 0.206 Angle : 0.644 9.057 5792 Z= 0.298 Chirality : 0.039 0.230 704 Planarity : 0.004 0.035 712 Dihedral : 4.195 22.088 586 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.38 % Allowed : 25.81 % Favored : 72.81 % 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: 1.57 (0.38), residues: 524 helix: 2.60 (0.28), residues: 328 sheet: -1.50 (0.71), residues: 60 loop : -1.79 (0.46), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 99 HIS 0.002 0.001 HIS A 247 PHE 0.022 0.001 PHE A 95 TYR 0.025 0.002 TYR A 319 ARG 0.003 0.000 ARG B 315 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 62 time to evaluate : 0.656 Fit side-chains REVERT: A 105 LEU cc_start: 0.8158 (mt) cc_final: 0.7793 (tp) REVERT: A 159 ASN cc_start: 0.8360 (m-40) cc_final: 0.8126 (t0) REVERT: A 266 PHE cc_start: 0.8780 (OUTLIER) cc_final: 0.7995 (m-10) REVERT: A 291 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8300 (pt0) REVERT: A 308 LYS cc_start: 0.8849 (mmmt) cc_final: 0.8527 (mttt) REVERT: B 70 CYS cc_start: 0.8668 (m) cc_final: 0.8405 (t) REVERT: B 105 LEU cc_start: 0.8260 (mt) cc_final: 0.7941 (tp) outliers start: 6 outliers final: 5 residues processed: 67 average time/residue: 0.1055 time to fit residues: 10.0993 Evaluate side-chains 67 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 61 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 271 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 chunk 28 optimal weight: 20.0000 chunk 36 optimal weight: 9.9990 chunk 1 optimal weight: 30.0000 chunk 34 optimal weight: 0.0370 overall best weight: 2.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 HIS ** 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 = 0.3585 r_free = 0.3585 target = 0.097799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.082043 restraints weight = 14716.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.084003 restraints weight = 8925.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.085345 restraints weight = 6363.793| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4270 Z= 0.170 Angle : 0.640 9.038 5792 Z= 0.293 Chirality : 0.038 0.171 704 Planarity : 0.004 0.034 712 Dihedral : 4.127 21.819 586 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.38 % Allowed : 26.73 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.38), residues: 524 helix: 2.64 (0.29), residues: 328 sheet: -1.56 (0.70), residues: 60 loop : -1.76 (0.46), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 99 HIS 0.001 0.000 HIS B 84 PHE 0.021 0.001 PHE A 95 TYR 0.026 0.001 TYR A 319 ARG 0.003 0.000 ARG B 315 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1087.99 seconds wall clock time: 20 minutes 24.14 seconds (1224.14 seconds total)