Starting phenix.real_space_refine (version: dev) on Tue Nov 29 13:09:24 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7da5_30623/11_2022/7da5_30623.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7da5_30623/11_2022/7da5_30623.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7da5_30623/11_2022/7da5_30623.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7da5_30623/11_2022/7da5_30623.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7da5_30623/11_2022/7da5_30623.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7da5_30623/11_2022/7da5_30623.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.004 sd= 0.066 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 4013 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2846 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 17, 'TRANS': 357} Chain breaks: 1 Chain: "B" Number of atoms: 1167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1167 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 158} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 205} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 534 Unresolved non-hydrogen angles: 684 Unresolved non-hydrogen dihedrals: 446 Unresolved non-hydrogen chiralities: 49 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 12, 'TYR:plan': 4, 'ASN:plan1': 7, 'TRP:plan': 4, 'HIS:plan': 3, 'PHE:plan': 5, 'GLU:plan': 16, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 284 Time building chain proxies: 2.80, per 1000 atoms: 0.70 Number of scatterers: 4013 At special positions: 0 Unit cell: (102.883, 54.8145, 114.689, 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 25 16.00 O 694 8.00 N 683 7.00 C 2611 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: 1.61 Conformation dependent library (CDL) restraints added in 806.9 milliseconds 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1056 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 4 sheets defined 62.6% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 17 through 34 removed outlier: 3.986A pdb=" N ALA A 21 " --> pdb=" O GLY A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 52 Processing helix chain 'A' and resid 55 through 84 removed outlier: 5.568A pdb=" N ILE A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N SER A 62 " --> pdb=" O VAL A 58 " (cutoff:3.500A) Proline residue: A 74 - end of helix Processing helix chain 'A' and resid 85 through 104 Processing helix chain 'A' and resid 109 through 139 Proline residue: A 130 - end of helix removed outlier: 3.505A pdb=" N PHE A 139 " --> pdb=" O ILE A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 172 removed outlier: 4.441A pdb=" N SER A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Proline residue: A 155 - end of helix Proline residue: A 163 - end of helix Processing helix chain 'A' and resid 173 through 192 removed outlier: 3.966A pdb=" N GLY A 183 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A 184 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N CYS A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 274 Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 279 through 290 removed outlier: 6.062A pdb=" N SER A 285 " --> pdb=" O LEU A 281 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N SER A 286 " --> pdb=" O VAL A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 321 removed outlier: 4.294A pdb=" N VAL A 311 " --> pdb=" O PHE A 307 " (cutoff:3.500A) Proline residue: A 314 - end of helix removed outlier: 3.933A pdb=" N ASN A 321 " --> pdb=" O GLY A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 329 Processing helix chain 'A' and resid 330 through 346 removed outlier: 4.102A pdb=" N SER A 336 " --> pdb=" O PHE A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 383 removed outlier: 3.995A pdb=" N TYR A 359 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N MET A 379 " --> pdb=" O PHE A 375 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ASP A 380 " --> pdb=" O GLU A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 415 removed outlier: 4.353A pdb=" N ILE A 396 " --> pdb=" O GLY A 392 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N VAL A 397 " --> pdb=" O LEU A 393 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N CYS A 400 " --> pdb=" O ILE A 396 " (cutoff:3.500A) Proline residue: A 401 - end of helix Proline residue: A 406 - end of helix removed outlier: 4.590A pdb=" N ARG A 411 " --> pdb=" O PRO A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 449 removed outlier: 3.771A pdb=" N TYR A 423 " --> pdb=" O TYR A 419 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ALA A 425 " --> pdb=" O TYR A 421 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL A 428 " --> pdb=" O TRP A 424 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N GLY A 442 " --> pdb=" O PHE A 438 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE A 443 " --> pdb=" O ILE A 439 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ALA A 449 " --> pdb=" O TYR A 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 81 No H-bonds generated for 'chain 'B' and resid 79 through 81' Processing helix chain 'B' and resid 153 through 156 Processing helix chain 'B' and resid 204 through 238 Proline residue: B 211 - end of helix removed outlier: 3.562A pdb=" N THR B 224 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Proline residue: B 235 - end of helix removed outlier: 4.542A pdb=" N VAL B 238 " --> pdb=" O LYS B 234 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 25 through 33 Processing sheet with id=AA2, first strand: chain 'B' and resid 60 through 63 removed outlier: 4.067A pdb=" N GLY B 95 " --> pdb=" O PHE B 89 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 108 through 109 removed outlier: 3.501A pdb=" N ARG B 166 " --> pdb=" O SER B 163 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 113 through 117 removed outlier: 6.449A pdb=" N GLU B 114 " --> pdb=" O ARG B 201 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ARG B 203 " --> pdb=" O GLU B 114 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N ILE B 116 " --> pdb=" O ARG B 203 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY B 192 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N TRP B 139 " --> pdb=" O LEU B 150 " (cutoff:3.500A) 301 hydrogen bonds defined for protein. 873 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: 1.17 Time building geometry restraints manager: 1.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 632 1.28 - 1.41: 1071 1.41 - 1.54: 2303 1.54 - 1.68: 58 1.68 - 1.81: 38 Bond restraints: 4102 Sorted by residual: bond pdb=" C PHE A 36 " pdb=" O PHE A 36 " ideal model delta sigma weight residual 1.238 1.144 0.094 1.28e-02 6.10e+03 5.39e+01 bond pdb=" CA ALA A 35 " pdb=" CB ALA A 35 " ideal model delta sigma weight residual 1.529 1.474 0.055 1.02e-02 9.61e+03 2.92e+01 bond pdb=" N PRO B 91 " pdb=" CD PRO B 91 " ideal model delta sigma weight residual 1.474 1.539 -0.065 1.40e-02 5.10e+03 2.14e+01 bond pdb=" N PRO B 132 " pdb=" CD PRO B 132 " ideal model delta sigma weight residual 1.474 1.535 -0.061 1.40e-02 5.10e+03 1.93e+01 bond pdb=" CA VAL B 131 " pdb=" C VAL B 131 " ideal model delta sigma weight residual 1.524 1.557 -0.033 8.30e-03 1.45e+04 1.61e+01 ... (remaining 4097 not shown) Histogram of bond angle deviations from ideal: 97.99 - 105.19: 82 105.19 - 112.39: 1973 112.39 - 119.60: 1393 119.60 - 126.80: 2100 126.80 - 134.01: 54 Bond angle restraints: 5602 Sorted by residual: angle pdb=" CA PRO B 91 " pdb=" N PRO B 91 " pdb=" CD PRO B 91 " ideal model delta sigma weight residual 111.50 97.99 13.51 1.40e+00 5.10e-01 9.32e+01 angle pdb=" CA PRO B 132 " pdb=" N PRO B 132 " pdb=" CD PRO B 132 " ideal model delta sigma weight residual 111.50 98.10 13.40 1.40e+00 5.10e-01 9.16e+01 angle pdb=" CA PRO B 93 " pdb=" N PRO B 93 " pdb=" CD PRO B 93 " ideal model delta sigma weight residual 111.50 99.09 12.41 1.40e+00 5.10e-01 7.86e+01 angle pdb=" C TYR A 34 " pdb=" CA TYR A 34 " pdb=" CB TYR A 34 " ideal model delta sigma weight residual 111.45 125.90 -14.45 1.72e+00 3.38e-01 7.06e+01 angle pdb=" C PHE A 36 " pdb=" N PRO A 37 " pdb=" CA PRO A 37 " ideal model delta sigma weight residual 119.84 129.71 -9.87 1.25e+00 6.40e-01 6.24e+01 ... (remaining 5597 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 2054 17.50 - 35.00: 208 35.00 - 52.50: 61 52.50 - 70.00: 11 70.00 - 87.50: 3 Dihedral angle restraints: 2337 sinusoidal: 675 harmonic: 1662 Sorted by residual: dihedral pdb=" C TYR A 34 " pdb=" N TYR A 34 " pdb=" CA TYR A 34 " pdb=" CB TYR A 34 " ideal model delta harmonic sigma weight residual -122.60 -142.16 19.56 0 2.50e+00 1.60e-01 6.12e+01 dihedral pdb=" C VAL B 50 " pdb=" N VAL B 50 " pdb=" CA VAL B 50 " pdb=" CB VAL B 50 " ideal model delta harmonic sigma weight residual -122.00 -139.09 17.09 0 2.50e+00 1.60e-01 4.67e+01 dihedral pdb=" N VAL B 50 " pdb=" C VAL B 50 " pdb=" CA VAL B 50 " pdb=" CB VAL B 50 " ideal model delta harmonic sigma weight residual 123.40 139.10 -15.70 0 2.50e+00 1.60e-01 3.94e+01 ... (remaining 2334 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 610 0.130 - 0.259: 37 0.259 - 0.389: 7 0.389 - 0.518: 4 0.518 - 0.648: 3 Chirality restraints: 661 Sorted by residual: chirality pdb=" CA TYR A 34 " pdb=" N TYR A 34 " pdb=" C TYR A 34 " pdb=" CB TYR A 34 " both_signs ideal model delta sigma weight residual False 2.51 1.86 0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" CA GLU B 172 " pdb=" N GLU B 172 " pdb=" C GLU B 172 " pdb=" CB GLU B 172 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.93e+00 chirality pdb=" CA VAL B 50 " pdb=" N VAL B 50 " pdb=" C VAL B 50 " pdb=" CB VAL B 50 " both_signs ideal model delta sigma weight residual False 2.44 1.88 0.56 2.00e-01 2.50e+01 7.77e+00 ... (remaining 658 not shown) Planarity restraints: 718 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 36 " -0.063 2.00e-02 2.50e+03 5.57e-02 5.44e+01 pdb=" CG PHE A 36 " 0.129 2.00e-02 2.50e+03 pdb=" CD1 PHE A 36 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE A 36 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 PHE A 36 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE A 36 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 36 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 36 " 0.032 2.00e-02 2.50e+03 6.63e-02 4.40e+01 pdb=" C PHE A 36 " -0.115 2.00e-02 2.50e+03 pdb=" O PHE A 36 " 0.044 2.00e-02 2.50e+03 pdb=" N PRO A 37 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 131 " 0.117 5.00e-02 4.00e+02 1.64e-01 4.29e+01 pdb=" N PRO B 132 " -0.282 5.00e-02 4.00e+02 pdb=" CA PRO B 132 " 0.098 5.00e-02 4.00e+02 pdb=" CD PRO B 132 " 0.067 5.00e-02 4.00e+02 ... (remaining 715 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.32: 15 2.32 - 2.96: 2199 2.96 - 3.61: 5766 3.61 - 4.25: 8424 4.25 - 4.90: 14144 Nonbonded interactions: 30548 Sorted by model distance: nonbonded pdb=" O ILE A 171 " pdb=" NE ARG B 203 " model vdw 1.673 2.520 nonbonded pdb=" CB HIS B 115 " pdb=" NH2 ARG B 203 " model vdw 1.936 3.520 nonbonded pdb=" O GLY A 73 " pdb=" OG SER A 76 " model vdw 1.959 2.440 nonbonded pdb=" CG2 THR A 54 " pdb=" OE2 GLU A 57 " model vdw 2.028 3.460 nonbonded pdb=" O PRO A 74 " pdb=" OG SER A 77 " model vdw 2.058 2.440 ... (remaining 30543 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 25 5.16 5 C 2611 2.51 5 N 683 2.21 5 O 694 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.650 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: 3.740 Check model and map are aligned: 0.060 Convert atoms to be neutral: 0.040 Process input model: 15.760 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5771 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.094 4102 Z= 0.539 Angle : 1.210 14.454 5602 Z= 0.816 Chirality : 0.087 0.648 661 Planarity : 0.010 0.164 718 Dihedral : 16.471 87.496 1281 Min Nonbonded Distance : 1.673 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.34 % Allowed : 9.06 % Favored : 90.60 % Rotamer Outliers : 10.06 % Cbeta Deviations : 1.89 % Peptide Plane: Cis-proline : 11.11 % 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: -3.63 (0.31), residues: 585 helix: -2.39 (0.24), residues: 342 sheet: 0.31 (0.53), residues: 94 loop : -3.80 (0.40), residues: 149 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 53 time to evaluate : 0.429 Fit side-chains outliers start: 33 outliers final: 17 residues processed: 79 average time/residue: 0.1935 time to fit residues: 18.4850 Evaluate side-chains 56 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 39 time to evaluate : 0.434 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.0406 time to fit residues: 1.8138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 20.0000 chunk 43 optimal weight: 8.9990 chunk 24 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 166 GLN A 260 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5848 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 4102 Z= 0.227 Angle : 0.699 8.390 5602 Z= 0.363 Chirality : 0.043 0.220 661 Planarity : 0.006 0.071 718 Dihedral : 4.758 27.726 621 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer Outliers : 3.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.69 (0.34), residues: 585 helix: -0.70 (0.27), residues: 353 sheet: 0.84 (0.52), residues: 101 loop : -3.61 (0.46), residues: 131 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 52 time to evaluate : 0.423 Fit side-chains outliers start: 11 outliers final: 4 residues processed: 60 average time/residue: 0.1263 time to fit residues: 10.1695 Evaluate side-chains 47 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 43 time to evaluate : 0.427 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0456 time to fit residues: 0.9094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 29 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 43 optimal weight: 50.0000 chunk 35 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 42 optimal weight: 10.0000 chunk 39 optimal weight: 50.0000 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 HIS ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6079 moved from start: 0.4201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 4102 Z= 0.313 Angle : 0.734 7.925 5602 Z= 0.389 Chirality : 0.046 0.182 661 Planarity : 0.006 0.074 718 Dihedral : 4.817 22.783 621 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.86 % Favored : 91.97 % Rotamer Outliers : 6.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.22 (0.34), residues: 585 helix: -0.46 (0.27), residues: 353 sheet: 1.39 (0.53), residues: 96 loop : -3.20 (0.48), residues: 136 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 60 time to evaluate : 0.428 Fit side-chains outliers start: 21 outliers final: 6 residues processed: 74 average time/residue: 0.1066 time to fit residues: 10.8426 Evaluate side-chains 62 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 56 time to evaluate : 0.426 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0427 time to fit residues: 1.0417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 52 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 46 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN ** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5979 moved from start: 0.4461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 4102 Z= 0.214 Angle : 0.652 7.158 5602 Z= 0.334 Chirality : 0.042 0.159 661 Planarity : 0.005 0.072 718 Dihedral : 4.415 23.626 621 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer Outliers : 2.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.48 (0.35), residues: 585 helix: 0.21 (0.28), residues: 350 sheet: 1.53 (0.53), residues: 96 loop : -2.95 (0.48), residues: 139 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 56 time to evaluate : 0.447 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 62 average time/residue: 0.1228 time to fit residues: 10.2654 Evaluate side-chains 57 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 53 time to evaluate : 0.429 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0385 time to fit residues: 0.8820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 41 optimal weight: 50.0000 chunk 23 optimal weight: 0.9990 chunk 47 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 chunk 50 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6028 moved from start: 0.4828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 4102 Z= 0.241 Angle : 0.680 8.178 5602 Z= 0.346 Chirality : 0.043 0.172 661 Planarity : 0.005 0.068 718 Dihedral : 4.408 24.218 621 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer Outliers : 2.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.31 (0.35), residues: 585 helix: 0.33 (0.28), residues: 349 sheet: 1.62 (0.53), residues: 96 loop : -2.82 (0.48), residues: 140 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 57 time to evaluate : 0.399 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 61 average time/residue: 0.1314 time to fit residues: 10.6646 Evaluate side-chains 58 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 54 time to evaluate : 0.429 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0472 time to fit residues: 0.9149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 13 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 18 optimal weight: 0.1980 chunk 29 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 40 optimal weight: 50.0000 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6002 moved from start: 0.5071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 4102 Z= 0.207 Angle : 0.648 8.526 5602 Z= 0.329 Chirality : 0.041 0.159 661 Planarity : 0.005 0.066 718 Dihedral : 4.275 23.738 621 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer Outliers : 2.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.03 (0.36), residues: 585 helix: 0.56 (0.28), residues: 348 sheet: 1.63 (0.53), residues: 96 loop : -2.62 (0.48), residues: 141 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 53 time to evaluate : 0.421 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 58 average time/residue: 0.1328 time to fit residues: 10.2260 Evaluate side-chains 54 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 50 time to evaluate : 0.422 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0495 time to fit residues: 0.9111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 31 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 22 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 38 optimal weight: 50.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN ** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5979 moved from start: 0.5284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 4102 Z= 0.203 Angle : 0.674 9.142 5602 Z= 0.333 Chirality : 0.041 0.162 661 Planarity : 0.005 0.066 718 Dihedral : 4.242 24.976 621 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer Outliers : 2.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.11 (0.36), residues: 585 helix: 0.66 (0.29), residues: 347 sheet: 1.67 (0.54), residues: 95 loop : -2.50 (0.49), residues: 143 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 56 time to evaluate : 0.438 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 61 average time/residue: 0.1276 time to fit residues: 10.5262 Evaluate side-chains 59 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 54 time to evaluate : 0.458 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0485 time to fit residues: 1.0772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 0.4980 chunk 5 optimal weight: 0.9990 chunk 43 optimal weight: 50.0000 chunk 50 optimal weight: 6.9990 chunk 53 optimal weight: 30.0000 chunk 48 optimal weight: 7.9990 chunk 52 optimal weight: 7.9990 chunk 31 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 15 optimal weight: 0.5980 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6027 moved from start: 0.5538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 4102 Z= 0.231 Angle : 0.703 12.049 5602 Z= 0.348 Chirality : 0.043 0.173 661 Planarity : 0.005 0.066 718 Dihedral : 4.273 23.676 621 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer Outliers : 1.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.04 (0.36), residues: 585 helix: 0.56 (0.28), residues: 347 sheet: 1.62 (0.55), residues: 95 loop : -2.37 (0.49), residues: 143 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 56 time to evaluate : 0.448 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 58 average time/residue: 0.1225 time to fit residues: 9.8082 Evaluate side-chains 57 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 55 time to evaluate : 0.439 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0557 time to fit residues: 0.7969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 0.3980 chunk 49 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 33 optimal weight: 0.0870 chunk 26 optimal weight: 1.9990 chunk 38 optimal weight: 50.0000 chunk 57 optimal weight: 0.8980 chunk 53 optimal weight: 20.0000 chunk 46 optimal weight: 3.9990 overall best weight: 0.8762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN ** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6003 moved from start: 0.5751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 4102 Z= 0.214 Angle : 0.710 12.592 5602 Z= 0.346 Chirality : 0.042 0.159 661 Planarity : 0.005 0.066 718 Dihedral : 4.215 23.796 621 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer Outliers : 0.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.16 (0.36), residues: 585 helix: 0.67 (0.29), residues: 347 sheet: 1.66 (0.55), residues: 95 loop : -2.34 (0.49), residues: 143 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 57 time to evaluate : 0.394 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 58 average time/residue: 0.1156 time to fit residues: 9.0608 Evaluate side-chains 54 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 53 time to evaluate : 0.374 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0373 time to fit residues: 0.5952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 4 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 chunk 14 optimal weight: 0.8980 chunk 42 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 46 optimal weight: 8.9990 chunk 19 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN ** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6028 moved from start: 0.5983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 4102 Z= 0.235 Angle : 0.745 13.049 5602 Z= 0.361 Chirality : 0.042 0.134 661 Planarity : 0.005 0.067 718 Dihedral : 4.313 23.915 621 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer Outliers : 0.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.09 (0.36), residues: 585 helix: 0.62 (0.29), residues: 347 sheet: 1.57 (0.55), residues: 95 loop : -2.36 (0.49), residues: 143 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 57 time to evaluate : 0.368 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 58 average time/residue: 0.1193 time to fit residues: 9.4059 Evaluate side-chains 52 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.429 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 40 optimal weight: 50.0000 chunk 2 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 52 optimal weight: 0.0970 chunk 30 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4636 r_free = 0.4636 target = 0.218217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.182840 restraints weight = 5695.697| |-----------------------------------------------------------------------------| r_work (start): 0.4280 rms_B_bonded: 2.66 r_work: 0.4272 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.4264 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work: 0.4255 rms_B_bonded: 2.50 restraints_weight: 0.1250 r_work: 0.4246 rms_B_bonded: 2.57 restraints_weight: 0.0625 r_work: 0.4236 rms_B_bonded: 2.68 restraints_weight: 0.0312 r_work: 0.4225 rms_B_bonded: 2.82 restraints_weight: 0.0156 r_work: 0.4214 rms_B_bonded: 3.00 restraints_weight: 0.0078 r_work: 0.4201 rms_B_bonded: 3.21 restraints_weight: 0.0039 r_work: 0.4188 rms_B_bonded: 3.47 restraints_weight: 0.0020 r_work: 0.4173 rms_B_bonded: 3.76 restraints_weight: 0.0010 r_work: 0.4156 rms_B_bonded: 4.11 restraints_weight: 0.0005 r_work: 0.4139 rms_B_bonded: 4.51 restraints_weight: 0.0002 r_work: 0.4119 rms_B_bonded: 4.98 restraints_weight: 0.0001 r_work (final): 0.4119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.6131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 4102 Z= 0.203 Angle : 0.701 12.693 5602 Z= 0.342 Chirality : 0.041 0.143 661 Planarity : 0.005 0.065 718 Dihedral : 4.185 23.982 621 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer Outliers : 0.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.21 (0.36), residues: 585 helix: 0.79 (0.29), residues: 347 sheet: 1.60 (0.55), residues: 95 loop : -2.51 (0.46), residues: 143 =============================================================================== Job complete usr+sys time: 1046.15 seconds wall clock time: 19 minutes 49.85 seconds (1189.85 seconds total)