Starting phenix.real_space_refine on Tue Feb 13 11:31:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgy_10188/02_2024/6sgy_10188.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgy_10188/02_2024/6sgy_10188.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgy_10188/02_2024/6sgy_10188.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgy_10188/02_2024/6sgy_10188.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgy_10188/02_2024/6sgy_10188.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgy_10188/02_2024/6sgy_10188.pdb" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 12 5.16 5 C 3632 2.51 5 N 996 2.21 5 O 1126 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 145": "OE1" <-> "OE2" Residue "A ASP 207": "OD1" <-> "OD2" Residue "A ASP 227": "OD1" <-> "OD2" Residue "A ASP 242": "OD1" <-> "OD2" Residue "A TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 313": "OD1" <-> "OD2" Residue "A PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 408": "OD1" <-> "OD2" Residue "A ASP 459": "OD1" <-> "OD2" Residue "B ASP 136": "OD1" <-> "OD2" Residue "B GLU 145": "OE1" <-> "OE2" Residue "B ASP 178": "OD1" <-> "OD2" Residue "B ASP 197": "OD1" <-> "OD2" Residue "B ASP 227": "OD1" <-> "OD2" Residue "B ASP 242": "OD1" <-> "OD2" Residue "B ASP 300": "OD1" <-> "OD2" Residue "B ASP 330": "OD1" <-> "OD2" Residue "B PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 344": "OE1" <-> "OE2" Residue "B PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 459": "OD1" <-> "OD2" Residue "B PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 5766 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 2883 Classifications: {'peptide': 402} Link IDs: {'PCIS': 2, 'PTRANS': 39, 'TRANS': 360} Chain: "B" Number of atoms: 2883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 2883 Classifications: {'peptide': 402} Link IDs: {'PCIS': 2, 'PTRANS': 39, 'TRANS': 360} Time building chain proxies: 3.74, per 1000 atoms: 0.65 Number of scatterers: 5766 At special positions: 0 Unit cell: (148.89, 61.683, 97.842, 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 12 16.00 O 1126 8.00 N 996 7.00 C 3632 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 177 " - pdb=" SG CYS A 376 " distance=2.02 Simple disulfide: pdb=" SG CYS B 177 " - pdb=" SG CYS B 376 " distance=2.02 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: 2.53 Conformation dependent library (CDL) restraints added in 1.3 seconds 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1452 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 15 sheets defined 17.2% alpha, 20.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 124 through 133 Processing helix chain 'A' and resid 142 through 147 removed outlier: 3.777A pdb=" N ILE A 146 " --> pdb=" O LYS A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 244 Processing helix chain 'A' and resid 257 through 262 Processing helix chain 'A' and resid 319 through 330 Processing helix chain 'A' and resid 341 through 348 Processing helix chain 'A' and resid 463 through 471 removed outlier: 4.100A pdb=" N VAL A 467 " --> pdb=" O ASP A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 485 removed outlier: 3.765A pdb=" N LEU A 484 " --> pdb=" O PRO A 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 133 Processing helix chain 'B' and resid 142 through 147 removed outlier: 3.986A pdb=" N ILE B 146 " --> pdb=" O LYS B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 244 removed outlier: 3.577A pdb=" N THR B 241 " --> pdb=" O ASP B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 264 removed outlier: 3.746A pdb=" N VAL B 264 " --> pdb=" O LEU B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 330 Processing helix chain 'B' and resid 341 through 348 Processing helix chain 'B' and resid 403 through 408 removed outlier: 3.595A pdb=" N THR B 406 " --> pdb=" O GLY B 403 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASP B 408 " --> pdb=" O HIS B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 471 removed outlier: 4.105A pdb=" N VAL B 467 " --> pdb=" O ASP B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 485 removed outlier: 3.703A pdb=" N LEU B 484 " --> pdb=" O PRO B 480 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 102 through 105 removed outlier: 6.678A pdb=" N ILE A 102 " --> pdb=" O THR A 139 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N VAL A 141 " --> pdb=" O ILE A 102 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N ALA A 104 " --> pdb=" O VAL A 141 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 189 through 191 Processing sheet with id=AA3, first strand: chain 'A' and resid 189 through 191 Processing sheet with id=AA4, first strand: chain 'A' and resid 230 through 232 Processing sheet with id=AA5, first strand: chain 'A' and resid 295 through 297 Processing sheet with id=AA6, first strand: chain 'A' and resid 408 through 409 Processing sheet with id=AA7, first strand: chain 'A' and resid 477 through 479 removed outlier: 4.258A pdb=" N LEU A 477 " --> pdb=" O GLY A 428 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL A 479 " --> pdb=" O PHE A 430 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N MET A 446 " --> pdb=" O ILE A 458 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 103 through 104 Processing sheet with id=AA9, first strand: chain 'B' and resid 112 through 115 Processing sheet with id=AB1, first strand: chain 'B' and resid 189 through 191 Processing sheet with id=AB2, first strand: chain 'B' and resid 189 through 191 Processing sheet with id=AB3, first strand: chain 'B' and resid 230 through 232 Processing sheet with id=AB4, first strand: chain 'B' and resid 315 through 317 removed outlier: 9.350A pdb=" N LEU B 340 " --> pdb=" O VAL B 295 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N VAL B 297 " --> pdb=" O LEU B 340 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 409 through 410 Processing sheet with id=AB6, first strand: chain 'B' and resid 477 through 479 removed outlier: 4.071A pdb=" N LEU B 477 " --> pdb=" O GLY B 428 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN B 432 " --> pdb=" O VAL B 479 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N MET B 446 " --> pdb=" O ILE B 458 " (cutoff:3.500A) 170 hydrogen bonds defined for protein. 462 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: 1.64 Time building geometry restraints manager: 2.58 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: 1955 1.34 - 1.46: 1038 1.46 - 1.57: 2899 1.57 - 1.69: 0 1.69 - 1.81: 20 Bond restraints: 5912 Sorted by residual: bond pdb=" C SER B 440 " pdb=" N PRO B 441 " ideal model delta sigma weight residual 1.331 1.402 -0.072 1.31e-02 5.83e+03 3.00e+01 bond pdb=" C SER A 440 " pdb=" N PRO A 441 " ideal model delta sigma weight residual 1.332 1.394 -0.062 1.32e-02 5.74e+03 2.24e+01 bond pdb=" N ALA A 252 " pdb=" CA ALA A 252 " ideal model delta sigma weight residual 1.464 1.425 0.039 9.80e-03 1.04e+04 1.60e+01 bond pdb=" C LEU A 288 " pdb=" N PRO A 289 " ideal model delta sigma weight residual 1.335 1.367 -0.032 9.40e-03 1.13e+04 1.15e+01 bond pdb=" CB TRP B 226 " pdb=" CG TRP B 226 " ideal model delta sigma weight residual 1.498 1.420 0.078 3.10e-02 1.04e+03 6.40e+00 ... (remaining 5907 not shown) Histogram of bond angle deviations from ideal: 98.57 - 107.31: 425 107.31 - 116.05: 3747 116.05 - 124.80: 3792 124.80 - 133.54: 167 133.54 - 142.29: 15 Bond angle restraints: 8146 Sorted by residual: angle pdb=" C ALA B 160 " pdb=" N PRO B 161 " pdb=" CA PRO B 161 " ideal model delta sigma weight residual 127.00 142.29 -15.29 2.40e+00 1.74e-01 4.06e+01 angle pdb=" C ALA B 160 " pdb=" N PRO B 161 " pdb=" CD PRO B 161 " ideal model delta sigma weight residual 120.60 107.24 13.36 2.20e+00 2.07e-01 3.69e+01 angle pdb=" N GLY B 457 " pdb=" CA GLY B 457 " pdb=" C GLY B 457 " ideal model delta sigma weight residual 110.42 119.33 -8.91 1.49e+00 4.50e-01 3.57e+01 angle pdb=" N LEU A 288 " pdb=" CA LEU A 288 " pdb=" C LEU A 288 " ideal model delta sigma weight residual 113.25 120.06 -6.81 1.30e+00 5.92e-01 2.74e+01 angle pdb=" N GLU B 285 " pdb=" CA GLU B 285 " pdb=" C GLU B 285 " ideal model delta sigma weight residual 110.91 116.88 -5.97 1.17e+00 7.31e-01 2.61e+01 ... (remaining 8141 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 3050 17.35 - 34.69: 413 34.69 - 52.03: 67 52.03 - 69.38: 9 69.38 - 86.72: 3 Dihedral angle restraints: 3542 sinusoidal: 1274 harmonic: 2268 Sorted by residual: dihedral pdb=" CA ASN B 184 " pdb=" C ASN B 184 " pdb=" N PRO B 185 " pdb=" CA PRO B 185 " ideal model delta harmonic sigma weight residual 180.00 126.23 53.77 0 5.00e+00 4.00e-02 1.16e+02 dihedral pdb=" CA ASP A 215 " pdb=" C ASP A 215 " pdb=" N ALA A 216 " pdb=" CA ALA A 216 " ideal model delta harmonic sigma weight residual -180.00 -133.63 -46.37 0 5.00e+00 4.00e-02 8.60e+01 dihedral pdb=" CA ALA B 418 " pdb=" C ALA B 418 " pdb=" N ASN B 419 " pdb=" CA ASN B 419 " ideal model delta harmonic sigma weight residual -180.00 -138.18 -41.82 0 5.00e+00 4.00e-02 7.00e+01 ... (remaining 3539 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 689 0.061 - 0.122: 212 0.122 - 0.183: 44 0.183 - 0.244: 8 0.244 - 0.304: 3 Chirality restraints: 956 Sorted by residual: chirality pdb=" CB ILE A 190 " pdb=" CA ILE A 190 " pdb=" CG1 ILE A 190 " pdb=" CG2 ILE A 190 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" CA LEU A 288 " pdb=" N LEU A 288 " pdb=" C LEU A 288 " pdb=" CB LEU A 288 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA PRO A 218 " pdb=" N PRO A 218 " pdb=" C PRO A 218 " pdb=" CB PRO A 218 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 953 not shown) Planarity restraints: 1094 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 184 " 0.071 5.00e-02 4.00e+02 1.08e-01 1.88e+01 pdb=" N PRO B 185 " -0.187 5.00e-02 4.00e+02 pdb=" CA PRO B 185 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO B 185 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 184 " -0.062 5.00e-02 4.00e+02 9.37e-02 1.40e+01 pdb=" N PRO A 185 " 0.162 5.00e-02 4.00e+02 pdb=" CA PRO A 185 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO A 185 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 424 " 0.061 5.00e-02 4.00e+02 9.09e-02 1.32e+01 pdb=" N PRO A 425 " -0.157 5.00e-02 4.00e+02 pdb=" CA PRO A 425 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 425 " 0.049 5.00e-02 4.00e+02 ... (remaining 1091 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1051 2.76 - 3.29: 5861 3.29 - 3.83: 10491 3.83 - 4.36: 11088 4.36 - 4.90: 17833 Nonbonded interactions: 46324 Sorted by model distance: nonbonded pdb=" O GLY A 181 " pdb=" OG1 THR A 188 " model vdw 2.225 2.440 nonbonded pdb=" O ASN B 124 " pdb=" OG SER B 127 " model vdw 2.252 2.440 nonbonded pdb=" O ASN A 124 " pdb=" OG SER A 127 " model vdw 2.265 2.440 nonbonded pdb=" OG1 THR A 433 " pdb=" O ALA A 443 " model vdw 2.266 2.440 nonbonded pdb=" OG SER A 450 " pdb=" OG1 THR A 452 " model vdw 2.274 2.440 ... (remaining 46319 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 Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' } Set refine NCS operators NCS operators will be refined. 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: 1.320 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: 5.740 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 19.790 Find NCS groups from input model: 0.470 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6585 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 : 0.007 0.078 5912 Z= 0.460 Angle : 1.349 15.285 8146 Z= 0.734 Chirality : 0.062 0.304 956 Planarity : 0.011 0.108 1094 Dihedral : 15.714 86.724 2084 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.75 % Favored : 87.25 % Rotamer: Outliers : 0.67 % Allowed : 15.17 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 1.39 % 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: -4.34 (0.24), residues: 800 helix: -3.19 (0.27), residues: 124 sheet: -2.86 (0.36), residues: 142 loop : -2.98 (0.24), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP A 174 HIS 0.010 0.002 HIS A 120 PHE 0.025 0.003 PHE B 447 TYR 0.025 0.004 TYR B 307 ARG 0.007 0.001 ARG B 352 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 82 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 MET cc_start: 0.8378 (mmp) cc_final: 0.8132 (mmp) REVERT: A 235 LEU cc_start: 0.6790 (pp) cc_final: 0.6579 (pp) outliers start: 2 outliers final: 0 residues processed: 84 average time/residue: 0.1759 time to fit residues: 17.2916 Evaluate side-chains 62 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 0.8980 chunk 60 optimal weight: 0.0270 chunk 33 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 32 optimal weight: 0.9990 chunk 62 optimal weight: 0.0270 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 72 optimal weight: 0.0370 overall best weight: 0.3974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 316 GLN ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 419 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6350 moved from start: 0.5547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5912 Z= 0.254 Angle : 0.885 9.210 8146 Z= 0.455 Chirality : 0.046 0.169 956 Planarity : 0.008 0.078 1094 Dihedral : 8.950 36.302 850 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 18.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.25 % Favored : 89.75 % Rotamer: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.28 % 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: -3.42 (0.26), residues: 800 helix: -2.23 (0.34), residues: 130 sheet: -2.17 (0.38), residues: 144 loop : -2.43 (0.25), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 379 HIS 0.006 0.001 HIS B 213 PHE 0.011 0.002 PHE B 487 TYR 0.013 0.002 TYR B 112 ARG 0.006 0.001 ARG B 254 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 MET cc_start: 0.8608 (mmp) cc_final: 0.8360 (mmp) REVERT: A 224 LEU cc_start: 0.7577 (tt) cc_final: 0.6610 (mt) REVERT: A 318 ILE cc_start: 0.7839 (pt) cc_final: 0.7517 (pt) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.1740 time to fit residues: 17.0702 Evaluate side-chains 70 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 60 optimal weight: 0.0470 chunk 49 optimal weight: 0.4980 chunk 20 optimal weight: 0.7980 chunk 72 optimal weight: 0.0670 chunk 78 optimal weight: 0.8980 chunk 64 optimal weight: 0.0010 chunk 24 optimal weight: 0.0870 chunk 58 optimal weight: 2.9990 chunk 71 optimal weight: 0.0020 overall best weight: 0.0408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN A 166 GLN A 208 HIS ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6183 moved from start: 0.6447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5912 Z= 0.218 Angle : 0.865 9.412 8146 Z= 0.423 Chirality : 0.046 0.145 956 Planarity : 0.008 0.075 1094 Dihedral : 7.841 30.953 850 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.50 % Favored : 89.50 % Rotamer: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.27), residues: 800 helix: -1.41 (0.38), residues: 130 sheet: -2.31 (0.37), residues: 148 loop : -2.10 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 379 HIS 0.007 0.001 HIS A 213 PHE 0.011 0.002 PHE B 149 TYR 0.011 0.002 TYR B 112 ARG 0.004 0.001 ARG A 151 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 TYR cc_start: 0.4596 (m-10) cc_final: 0.4211 (m-10) REVERT: A 224 LEU cc_start: 0.7368 (tt) cc_final: 0.6500 (mt) REVERT: A 318 ILE cc_start: 0.7646 (pt) cc_final: 0.6977 (pt) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.1602 time to fit residues: 16.0541 Evaluate side-chains 70 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 0.0980 chunk 37 optimal weight: 0.3980 chunk 8 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 77 optimal weight: 0.0170 chunk 38 optimal weight: 0.0270 chunk 69 optimal weight: 0.9990 chunk 20 optimal weight: 0.0050 chunk 64 optimal weight: 0.0570 overall best weight: 0.0408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 166 GLN ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 378 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6108 moved from start: 0.6808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5912 Z= 0.213 Angle : 0.820 9.312 8146 Z= 0.401 Chirality : 0.044 0.136 956 Planarity : 0.007 0.070 1094 Dihedral : 7.126 30.160 850 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.25 % Favored : 90.75 % Rotamer: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.29), residues: 800 helix: -0.41 (0.44), residues: 118 sheet: -2.13 (0.33), residues: 180 loop : -1.98 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 379 HIS 0.006 0.002 HIS B 213 PHE 0.010 0.001 PHE A 487 TYR 0.011 0.002 TYR A 112 ARG 0.010 0.001 ARG A 254 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 112 TYR cc_start: 0.4956 (m-10) cc_final: 0.4501 (m-10) REVERT: B 164 MET cc_start: 0.8383 (mmp) cc_final: 0.8147 (mmp) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1595 time to fit residues: 15.1973 Evaluate side-chains 65 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 57 optimal weight: 0.4980 chunk 31 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 53 optimal weight: 0.0980 chunk 0 optimal weight: 3.9990 chunk 39 optimal weight: 0.0870 chunk 69 optimal weight: 0.5980 chunk 19 optimal weight: 0.0970 chunk 26 optimal weight: 0.0170 overall best weight: 0.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6094 moved from start: 0.7243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5912 Z= 0.195 Angle : 0.770 9.691 8146 Z= 0.374 Chirality : 0.044 0.133 956 Planarity : 0.007 0.068 1094 Dihedral : 6.478 27.172 850 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.25 % Favored : 88.75 % Rotamer: Outliers : 0.33 % Allowed : 2.67 % Favored : 97.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.28), residues: 800 helix: -0.80 (0.43), residues: 118 sheet: -2.44 (0.35), residues: 150 loop : -2.04 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 379 HIS 0.007 0.002 HIS A 213 PHE 0.010 0.001 PHE A 284 TYR 0.008 0.001 TYR A 112 ARG 0.004 0.000 ARG A 238 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 78 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 112 TYR cc_start: 0.4733 (m-80) cc_final: 0.4471 (m-10) REVERT: B 318 ILE cc_start: 0.6984 (pt) cc_final: 0.6513 (pt) outliers start: 1 outliers final: 1 residues processed: 78 average time/residue: 0.1580 time to fit residues: 14.6693 Evaluate side-chains 64 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 63 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 0.0270 chunk 15 optimal weight: 0.0870 chunk 45 optimal weight: 0.0060 chunk 19 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 6 optimal weight: 0.2980 chunk 25 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 74 optimal weight: 0.0570 overall best weight: 0.0950 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 166 GLN ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6067 moved from start: 0.7536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5912 Z= 0.200 Angle : 0.767 9.557 8146 Z= 0.377 Chirality : 0.043 0.134 956 Planarity : 0.007 0.067 1094 Dihedral : 6.281 28.547 850 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.25 % Favored : 88.75 % Rotamer: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.95 (0.27), residues: 800 helix: -0.80 (0.41), residues: 120 sheet: -2.12 (0.35), residues: 174 loop : -2.29 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 379 HIS 0.004 0.001 HIS B 378 PHE 0.011 0.001 PHE B 284 TYR 0.007 0.001 TYR B 112 ARG 0.005 0.001 ARG B 352 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 164 MET cc_start: 0.8143 (mmp) cc_final: 0.7914 (mmp) REVERT: B 318 ILE cc_start: 0.7043 (pt) cc_final: 0.6565 (pt) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1657 time to fit residues: 14.8134 Evaluate side-chains 64 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 56 optimal weight: 0.0870 chunk 43 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 35 optimal weight: 0.0010 chunk 30 optimal weight: 0.2980 chunk 46 optimal weight: 0.5980 overall best weight: 0.3164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 166 GLN B 219 ASN ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6117 moved from start: 0.7812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5912 Z= 0.222 Angle : 0.778 9.490 8146 Z= 0.384 Chirality : 0.043 0.131 956 Planarity : 0.007 0.064 1094 Dihedral : 6.164 29.999 850 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.50 % Favored : 88.50 % Rotamer: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: -3.04 (0.27), residues: 800 helix: -0.74 (0.42), residues: 120 sheet: -2.33 (0.34), residues: 180 loop : -2.31 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 379 HIS 0.007 0.002 HIS B 378 PHE 0.009 0.002 PHE A 284 TYR 0.014 0.002 TYR A 112 ARG 0.004 0.001 ARG A 200 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 112 TYR cc_start: 0.4238 (m-10) cc_final: 0.3868 (m-10) REVERT: B 318 ILE cc_start: 0.7166 (pt) cc_final: 0.6710 (pt) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1792 time to fit residues: 16.0641 Evaluate side-chains 60 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 0.0470 chunk 15 optimal weight: 1.9990 chunk 14 optimal weight: 0.0670 chunk 49 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 38 optimal weight: 0.3980 chunk 7 optimal weight: 0.4980 chunk 60 optimal weight: 0.0020 chunk 70 optimal weight: 0.0030 chunk 73 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 overall best weight: 0.1034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6053 moved from start: 0.7929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5912 Z= 0.203 Angle : 0.781 9.823 8146 Z= 0.378 Chirality : 0.044 0.133 956 Planarity : 0.006 0.062 1094 Dihedral : 5.990 27.838 850 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.75 % Favored : 88.25 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: -3.00 (0.27), residues: 800 helix: -0.83 (0.40), residues: 120 sheet: -2.26 (0.33), residues: 176 loop : -2.28 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 379 HIS 0.006 0.001 HIS B 378 PHE 0.011 0.001 PHE A 284 TYR 0.011 0.001 TYR A 112 ARG 0.003 0.000 ARG B 200 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 112 TYR cc_start: 0.4302 (m-10) cc_final: 0.3651 (m-10) REVERT: B 315 LEU cc_start: 0.5461 (mm) cc_final: 0.5106 (mm) REVERT: B 318 ILE cc_start: 0.7033 (pt) cc_final: 0.6441 (pt) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1829 time to fit residues: 17.2492 Evaluate side-chains 61 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 0.0030 chunk 73 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 31 optimal weight: 0.0030 chunk 56 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 chunk 46 optimal weight: 0.0570 overall best weight: 0.2918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 166 GLN ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6066 moved from start: 0.8084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5912 Z= 0.205 Angle : 0.756 9.495 8146 Z= 0.368 Chirality : 0.043 0.133 956 Planarity : 0.006 0.063 1094 Dihedral : 5.830 26.481 850 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.00 % Favored : 89.00 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.27), residues: 800 helix: -0.80 (0.41), residues: 120 sheet: -1.97 (0.37), residues: 156 loop : -2.25 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 379 HIS 0.005 0.002 HIS B 378 PHE 0.010 0.002 PHE A 149 TYR 0.007 0.001 TYR A 429 ARG 0.002 0.000 ARG B 254 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 315 LEU cc_start: 0.4973 (mm) cc_final: 0.4520 (mm) REVERT: B 318 ILE cc_start: 0.7109 (pt) cc_final: 0.6556 (pt) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1761 time to fit residues: 16.0356 Evaluate side-chains 58 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 63 optimal weight: 0.0570 chunk 6 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 50 optimal weight: 8.9990 chunk 67 optimal weight: 0.1980 chunk 19 optimal weight: 0.9990 overall best weight: 0.6102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6162 moved from start: 0.8038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 5912 Z= 0.213 Angle : 0.761 8.672 8146 Z= 0.374 Chirality : 0.043 0.134 956 Planarity : 0.006 0.064 1094 Dihedral : 5.825 29.264 850 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.50 % Favored : 88.50 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.27), residues: 800 helix: -1.10 (0.39), residues: 120 sheet: -2.12 (0.32), residues: 202 loop : -2.22 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 379 HIS 0.006 0.002 HIS B 378 PHE 0.010 0.002 PHE A 430 TYR 0.010 0.002 TYR A 112 ARG 0.005 0.001 ARG A 151 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 164 MET cc_start: 0.8186 (mmp) cc_final: 0.7977 (mmp) REVERT: B 315 LEU cc_start: 0.5079 (mm) cc_final: 0.4722 (mm) REVERT: B 318 ILE cc_start: 0.7190 (pt) cc_final: 0.6651 (pt) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.2269 time to fit residues: 19.8018 Evaluate side-chains 58 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 1.9990 chunk 9 optimal weight: 0.0570 chunk 17 optimal weight: 0.0870 chunk 63 optimal weight: 0.0270 chunk 26 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 8 optimal weight: 0.0040 chunk 11 optimal weight: 0.0170 chunk 55 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 overall best weight: 0.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 166 GLN ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.090945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.070854 restraints weight = 13222.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.073248 restraints weight = 9529.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.075221 restraints weight = 7370.746| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.8307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 5912 Z= 0.216 Angle : 0.801 9.909 8146 Z= 0.387 Chirality : 0.044 0.132 956 Planarity : 0.006 0.060 1094 Dihedral : 5.690 30.350 850 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.50 % Favored : 89.50 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.27), residues: 800 helix: -0.92 (0.41), residues: 120 sheet: -2.05 (0.35), residues: 182 loop : -2.24 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 379 HIS 0.007 0.002 HIS B 378 PHE 0.013 0.002 PHE A 430 TYR 0.019 0.002 TYR B 112 ARG 0.006 0.001 ARG B 163 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1488.62 seconds wall clock time: 27 minutes 30.04 seconds (1650.04 seconds total)