Starting phenix.real_space_refine on Thu Dec 7 20:05:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nt6_0503/12_2023/6nt6_0503.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nt6_0503/12_2023/6nt6_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_0503/12_2023/6nt6_0503.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nt6_0503/12_2023/6nt6_0503.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nt6_0503/12_2023/6nt6_0503.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nt6_0503/12_2023/6nt6_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: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 2.26, per 1000 atoms: 0.54 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: 1.20 Conformation dependent library (CDL) restraints added in 569.6 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: 0.31 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: 0.84 Time building geometry restraints manager: 1.34 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: 0.010 Extract box with map and model: 1.190 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 12.590 Find NCS groups from input model: 0.170 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:2.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.520 ------------------------------------------------------------------------------- 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 outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.1525 time to fit residues: 28.2598 Evaluate side-chains 63 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.502 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6943 ------------------------------------------------------------------------------- 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: 8.9990 chunk 13 optimal weight: 0.5980 chunk 27 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 42 optimal weight: 20.0000 chunk 16 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 31 optimal weight: 8.9990 chunk 49 optimal weight: 7.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- 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: 0.8097 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4270 Z= 0.267 Angle : 0.729 8.224 5792 Z= 0.346 Chirality : 0.041 0.170 704 Planarity : 0.005 0.038 712 Dihedral : 4.971 15.439 586 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.76 % Allowed : 20.05 % Favored : 77.19 % 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: -0.78 (0.35), residues: 524 helix: 0.68 (0.28), residues: 318 sheet: -1.77 (0.63), residues: 56 loop : -2.57 (0.42), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 166 HIS 0.005 0.001 HIS A 204 PHE 0.011 0.001 PHE A 95 TYR 0.006 0.001 TYR B 226 ARG 0.002 0.000 ARG A 294 *********************** 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 87 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 75 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 85 average time/residue: 0.1370 time to fit residues: 15.5071 Evaluate side-chains 62 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 54 time to evaluate : 0.540 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0412 time to fit residues: 1.2548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 0.0040 chunk 15 optimal weight: 20.0000 chunk 40 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 13 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 48 optimal weight: 0.0980 chunk 16 optimal weight: 8.9990 chunk 39 optimal weight: 6.9990 overall best weight: 1.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 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: 0.8037 moved from start: 0.3147 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= 0.167 Angle : 0.649 10.478 5792 Z= 0.303 Chirality : 0.039 0.168 704 Planarity : 0.004 0.031 712 Dihedral : 4.630 17.285 586 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.15 % Allowed : 19.35 % Favored : 79.49 % 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: 0.08 (0.36), residues: 524 helix: 1.43 (0.29), residues: 322 sheet: -1.65 (0.66), residues: 56 loop : -2.40 (0.42), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 336 HIS 0.002 0.000 HIS B 337 PHE 0.005 0.001 PHE B 36 TYR 0.020 0.001 TYR B 319 ARG 0.001 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 91 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 86 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 90 average time/residue: 0.1265 time to fit residues: 15.0247 Evaluate side-chains 64 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 63 time to evaluate : 0.447 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0403 time to fit residues: 0.6690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 chunk 32 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 52 optimal weight: 10.0000 chunk 46 optimal weight: 20.0000 chunk 14 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 337 HIS ** 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: 0.8083 moved from start: 0.3581 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= 0.233 Angle : 0.672 11.490 5792 Z= 0.310 Chirality : 0.038 0.142 704 Planarity : 0.004 0.039 712 Dihedral : 4.676 19.123 586 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.53 % Allowed : 20.51 % Favored : 76.96 % 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: 0.50 (0.37), residues: 524 helix: 1.75 (0.29), residues: 326 sheet: -1.49 (0.69), residues: 56 loop : -2.33 (0.44), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 99 HIS 0.003 0.001 HIS A 83 PHE 0.020 0.002 PHE A 95 TYR 0.008 0.001 TYR B 314 ARG 0.002 0.000 ARG A 294 *********************** 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 78 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 67 time to evaluate : 0.523 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 74 average time/residue: 0.1303 time to fit residues: 13.1535 Evaluate side-chains 63 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 56 time to evaluate : 0.530 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0443 time to fit residues: 1.2550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 26 optimal weight: 0.1980 chunk 46 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 17 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 HIS ** 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: 0.8067 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4270 Z= 0.190 Angle : 0.637 10.319 5792 Z= 0.295 Chirality : 0.037 0.145 704 Planarity : 0.004 0.038 712 Dihedral : 4.573 17.937 586 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.15 % Allowed : 21.66 % Favored : 77.19 % 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: 0.84 (0.38), residues: 524 helix: 2.01 (0.29), residues: 326 sheet: -1.31 (0.72), residues: 56 loop : -2.20 (0.45), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 99 HIS 0.001 0.001 HIS B 83 PHE 0.031 0.002 PHE B 95 TYR 0.027 0.002 TYR A 319 ARG 0.002 0.000 ARG A 294 *********************** 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 68 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 63 time to evaluate : 0.493 Fit side-chains outliers start: 5 outliers final: 0 residues processed: 67 average time/residue: 0.1211 time to fit residues: 11.1208 Evaluate side-chains 57 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.517 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 9.9990 chunk 30 optimal weight: 0.9980 chunk 12 optimal weight: 10.0000 chunk 52 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 27 optimal weight: 20.0000 chunk 50 optimal weight: 4.9990 chunk 5 optimal weight: 10.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 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: 0.8082 moved from start: 0.4066 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= 0.223 Angle : 0.653 8.758 5792 Z= 0.304 Chirality : 0.038 0.138 704 Planarity : 0.004 0.032 712 Dihedral : 4.552 17.244 586 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.07 % Allowed : 21.66 % Favored : 76.27 % 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: 0.85 (0.38), residues: 524 helix: 2.03 (0.29), residues: 326 sheet: -1.64 (0.70), residues: 60 loop : -2.04 (0.47), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 99 HIS 0.003 0.001 HIS A 337 PHE 0.025 0.002 PHE B 95 TYR 0.009 0.001 TYR B 314 ARG 0.002 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 71 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 62 time to evaluate : 0.510 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 66 average time/residue: 0.1290 time to fit residues: 11.5081 Evaluate side-chains 59 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 55 time to evaluate : 0.509 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0416 time to fit residues: 0.9757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 0.8980 chunk 24 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 15 optimal weight: 20.0000 chunk 10 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 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: 0.8057 moved from start: 0.4174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4270 Z= 0.169 Angle : 0.631 8.597 5792 Z= 0.291 Chirality : 0.037 0.143 704 Planarity : 0.004 0.031 712 Dihedral : 4.406 16.496 586 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.46 % Allowed : 23.96 % Favored : 75.58 % 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: 1.09 (0.38), residues: 524 helix: 2.17 (0.29), residues: 328 sheet: -1.60 (0.69), residues: 60 loop : -1.84 (0.48), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 99 HIS 0.002 0.001 HIS A 337 PHE 0.022 0.001 PHE B 95 TYR 0.013 0.001 TYR B 319 ARG 0.002 0.000 ARG A 294 *********************** 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 65 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 63 time to evaluate : 0.506 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 64 average time/residue: 0.1121 time to fit residues: 10.0923 Evaluate side-chains 56 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 55 time to evaluate : 0.491 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0432 time to fit residues: 0.7436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 4.9990 chunk 25 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 49 optimal weight: 0.0010 chunk 45 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 21 optimal weight: 0.3980 chunk 38 optimal weight: 0.8980 overall best weight: 0.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 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: 0.8010 moved from start: 0.4385 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= 0.145 Angle : 0.622 8.709 5792 Z= 0.287 Chirality : 0.037 0.144 704 Planarity : 0.004 0.034 712 Dihedral : 4.216 14.733 586 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.00 % Allowed : 24.65 % Favored : 75.35 % 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: 1.21 (0.38), residues: 524 helix: 2.32 (0.29), residues: 326 sheet: -1.57 (0.68), residues: 60 loop : -1.89 (0.47), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 99 HIS 0.002 0.000 HIS A 337 PHE 0.022 0.001 PHE B 95 TYR 0.010 0.001 TYR A 314 ARG 0.001 0.000 ARG A 51 *********************** 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 68 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.1163 time to fit residues: 10.9922 Evaluate side-chains 60 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.465 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 9.9990 chunk 43 optimal weight: 0.5980 chunk 45 optimal weight: 9.9990 chunk 48 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 24 optimal weight: 6.9990 chunk 35 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 49 optimal weight: 8.9990 chunk 42 optimal weight: 20.0000 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 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: 0.8011 moved from start: 0.4480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4270 Z= 0.148 Angle : 0.650 9.397 5792 Z= 0.290 Chirality : 0.037 0.164 704 Planarity : 0.004 0.032 712 Dihedral : 4.250 20.143 586 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.00 % Allowed : 26.04 % Favored : 73.96 % 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: 1.37 (0.38), residues: 524 helix: 2.43 (0.29), residues: 326 sheet: -1.41 (0.71), residues: 60 loop : -1.82 (0.47), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 99 HIS 0.002 0.000 HIS A 337 PHE 0.021 0.001 PHE B 95 TYR 0.017 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 65 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.542 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.1224 time to fit residues: 11.1457 Evaluate side-chains 58 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.499 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 9.9990 chunk 33 optimal weight: 7.9990 chunk 26 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 13 optimal weight: 0.6980 chunk 39 optimal weight: 9.9990 chunk 6 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 42 optimal weight: 20.0000 chunk 17 optimal weight: 0.9980 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 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: 0.8053 moved from start: 0.4542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4270 Z= 0.190 Angle : 0.655 8.931 5792 Z= 0.298 Chirality : 0.038 0.133 704 Planarity : 0.004 0.036 712 Dihedral : 4.282 18.851 586 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.23 % Allowed : 25.58 % 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: 1.45 (0.38), residues: 524 helix: 2.53 (0.29), residues: 326 sheet: -1.42 (0.72), residues: 60 loop : -1.90 (0.47), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 99 HIS 0.002 0.001 HIS B 247 PHE 0.019 0.001 PHE B 95 TYR 0.009 0.001 TYR B 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 62 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 61 time to evaluate : 0.518 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 62 average time/residue: 0.1283 time to fit residues: 10.8593 Evaluate side-chains 54 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.500 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 7 optimal weight: 0.0000 chunk 37 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 30 optimal weight: 8.9990 chunk 49 optimal weight: 0.0570 chunk 28 optimal weight: 10.0000 chunk 36 optimal weight: 8.9990 chunk 1 optimal weight: 20.0000 chunk 34 optimal weight: 0.0030 overall best weight: 0.6116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** 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 = 0.3610 r_free = 0.3610 target = 0.099574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.083557 restraints weight = 14808.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.085658 restraints weight = 8980.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.087049 restraints weight = 6381.124| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.4681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4270 Z= 0.144 Angle : 0.652 9.257 5792 Z= 0.292 Chirality : 0.037 0.141 704 Planarity : 0.003 0.032 712 Dihedral : 4.171 19.240 586 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.00 % Allowed : 26.50 % Favored : 73.50 % 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: 1.44 (0.38), residues: 524 helix: 2.50 (0.28), residues: 326 sheet: -1.32 (0.73), residues: 60 loop : -1.89 (0.46), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 99 HIS 0.001 0.000 HIS A 26 PHE 0.020 0.001 PHE B 95 TYR 0.017 0.001 TYR B 319 ARG 0.002 0.000 ARG B 315 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 981.64 seconds wall clock time: 21 minutes 18.72 seconds (1278.72 seconds total)