Starting phenix.real_space_refine (version: 1.21rc1) on Mon Oct 2 23:48:52 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ym8_33924/10_2023/7ym8_33924.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ym8_33924/10_2023/7ym8_33924.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ym8_33924/10_2023/7ym8_33924.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ym8_33924/10_2023/7ym8_33924.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ym8_33924/10_2023/7ym8_33924.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ym8_33924/10_2023/7ym8_33924.pdb" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.109 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 26 5.16 5 C 2805 2.51 5 N 704 2.21 5 O 752 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 204": "OE1" <-> "OE2" Residue "A PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 4287 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 1238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1238 Classifications: {'peptide': 169} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 1, 'TRANS': 167} Chain breaks: 2 Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 120 Chain: "A" Number of atoms: 2108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2108 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 14, 'TRANS': 256} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 887 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 113} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'J5C': 1, 'Y01': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.10, per 1000 atoms: 0.72 Number of scatterers: 4287 At special positions: 0 Unit cell: (59.5375, 58.455, 138.56, 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 26 16.00 O 752 8.00 N 704 7.00 C 2805 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 99 " - pdb=" SG CYS A 176 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 94 " distance=2.03 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: 1.69 Conformation dependent library (CDL) restraints added in 637.9 milliseconds 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1038 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 3 sheets defined 51.8% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'B' and resid 27 through 33 Processing helix chain 'B' and resid 77 through 82 removed outlier: 3.666A pdb=" N CYS B 81 " --> pdb=" O LYS B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 113 Processing helix chain 'B' and resid 128 through 133 removed outlier: 3.708A pdb=" N ALA B 132 " --> pdb=" O GLN B 128 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU B 133 " --> pdb=" O ASP B 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 128 through 133' Processing helix chain 'B' and resid 169 through 184 removed outlier: 4.243A pdb=" N PHE B 174 " --> pdb=" O ARG B 170 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N ILE B 175 " --> pdb=" O ALA B 171 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG B 176 " --> pdb=" O LYS B 172 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE B 179 " --> pdb=" O ILE B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 225 removed outlier: 3.722A pdb=" N ARG B 208 " --> pdb=" O GLU B 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 53 removed outlier: 3.586A pdb=" N ILE A 48 " --> pdb=" O ASN A 44 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL A 51 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N CYS A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 79 removed outlier: 3.664A pdb=" N ILE A 65 " --> pdb=" O THR A 61 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU A 68 " --> pdb=" O TYR A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 90 Processing helix chain 'A' and resid 95 through 129 Processing helix chain 'A' and resid 141 through 159 Processing helix chain 'A' and resid 184 through 211 removed outlier: 5.603A pdb=" N LEU A 195 " --> pdb=" O GLY A 191 " (cutoff:3.500A) Proline residue: A 196 - end of helix Processing helix chain 'A' and resid 263 through 286 removed outlier: 3.931A pdb=" N GLU A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LYS A 269 " --> pdb=" O SER A 265 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE A 281 " --> pdb=" O VAL A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 Proline residue: A 293 - end of helix Processing helix chain 'A' and resid 304 through 326 removed outlier: 3.775A pdb=" N PHE A 308 " --> pdb=" O SER A 304 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLY A 315 " --> pdb=" O VAL A 311 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TYR A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N SER A 319 " --> pdb=" O GLY A 315 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N CYS A 320 " --> pdb=" O TYR A 316 " (cutoff:3.500A) Proline residue: A 323 - end of helix Processing helix chain 'A' and resid 327 through 329 No H-bonds generated for 'chain 'A' and resid 327 through 329' Processing helix chain 'A' and resid 330 through 341 removed outlier: 3.875A pdb=" N GLN A 338 " --> pdb=" O LYS A 334 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN A 339 " --> pdb=" O LYS A 335 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 52 through 58 removed outlier: 9.826A pdb=" N ALA B 87 " --> pdb=" O THR B 15 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ARG B 17 " --> pdb=" O ALA B 87 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N ILE B 89 " --> pdb=" O ARG B 17 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU B 19 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N VAL B 91 " --> pdb=" O LEU B 19 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 6 through 7 Processing sheet with id=AA3, first strand: chain 'D' and resid 11 through 13 removed outlier: 3.585A pdb=" N SER D 115 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N MET D 34 " --> pdb=" O GLY D 50 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N GLY D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) 240 hydrogen bonds defined for protein. 705 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: 1.14 Time building geometry restraints manager: 1.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 669 1.32 - 1.44: 1248 1.44 - 1.56: 2438 1.56 - 1.68: 1 1.68 - 1.81: 35 Bond restraints: 4391 Sorted by residual: bond pdb=" C9 J5C A 501 " pdb=" N13 J5C A 501 " ideal model delta sigma weight residual 1.277 1.463 -0.186 2.00e-02 2.50e+03 8.67e+01 bond pdb=" C9 J5C A 501 " pdb=" N10 J5C A 501 " ideal model delta sigma weight residual 1.373 1.465 -0.092 2.00e-02 2.50e+03 2.11e+01 bond pdb=" C11 J5C A 501 " pdb=" C12 J5C A 501 " ideal model delta sigma weight residual 1.540 1.490 0.050 2.00e-02 2.50e+03 6.37e+00 bond pdb=" C5 J5C A 501 " pdb=" O15 J5C A 501 " ideal model delta sigma weight residual 1.356 1.400 -0.044 2.00e-02 2.50e+03 4.89e+00 bond pdb=" C MET A 292 " pdb=" N PRO A 293 " ideal model delta sigma weight residual 1.334 1.376 -0.043 2.34e-02 1.83e+03 3.31e+00 ... (remaining 4386 not shown) Histogram of bond angle deviations from ideal: 98.32 - 105.47: 67 105.47 - 112.62: 2230 112.62 - 119.78: 1532 119.78 - 126.93: 2101 126.93 - 134.08: 59 Bond angle restraints: 5989 Sorted by residual: angle pdb=" C ARG B 117 " pdb=" N THR B 118 " pdb=" CA THR B 118 " ideal model delta sigma weight residual 122.46 127.56 -5.10 1.41e+00 5.03e-01 1.31e+01 angle pdb=" N LEU A 80 " pdb=" CA LEU A 80 " pdb=" C LEU A 80 " ideal model delta sigma weight residual 109.81 117.34 -7.53 2.21e+00 2.05e-01 1.16e+01 angle pdb=" CA THR B 118 " pdb=" CB THR B 118 " pdb=" CG2 THR B 118 " ideal model delta sigma weight residual 110.50 115.96 -5.46 1.70e+00 3.46e-01 1.03e+01 angle pdb=" N ASN A 322 " pdb=" CA ASN A 322 " pdb=" C ASN A 322 " ideal model delta sigma weight residual 113.16 117.48 -4.32 1.42e+00 4.96e-01 9.26e+00 angle pdb=" N10 J5C A 501 " pdb=" C9 J5C A 501 " pdb=" N13 J5C A 501 " ideal model delta sigma weight residual 116.22 107.31 8.91 3.00e+00 1.11e-01 8.82e+00 ... (remaining 5984 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.64: 2227 16.64 - 33.29: 224 33.29 - 49.93: 62 49.93 - 66.57: 16 66.57 - 83.21: 4 Dihedral angle restraints: 2533 sinusoidal: 918 harmonic: 1615 Sorted by residual: dihedral pdb=" CB CYS D 22 " pdb=" SG CYS D 22 " pdb=" SG CYS D 94 " pdb=" CB CYS D 94 " ideal model delta sinusoidal sigma weight residual 93.00 59.87 33.13 1 1.00e+01 1.00e-02 1.56e+01 dihedral pdb=" CA ILE A 325 " pdb=" C ILE A 325 " pdb=" N TYR A 326 " pdb=" CA TYR A 326 " ideal model delta harmonic sigma weight residual -180.00 -161.10 -18.90 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA ILE A 126 " pdb=" C ILE A 126 " pdb=" N GLY A 127 " pdb=" CA GLY A 127 " ideal model delta harmonic sigma weight residual 180.00 163.85 16.15 0 5.00e+00 4.00e-02 1.04e+01 ... (remaining 2530 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 411 0.038 - 0.077: 191 0.077 - 0.115: 67 0.115 - 0.154: 16 0.154 - 0.192: 7 Chirality restraints: 692 Sorted by residual: chirality pdb=" CB VAL B 85 " pdb=" CA VAL B 85 " pdb=" CG1 VAL B 85 " pdb=" CG2 VAL B 85 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.21e-01 chirality pdb=" CA THR B 118 " pdb=" N THR B 118 " pdb=" C THR B 118 " pdb=" CB THR B 118 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.19 2.00e-01 2.50e+01 8.78e-01 chirality pdb=" CB ILE A 126 " pdb=" CA ILE A 126 " pdb=" CG1 ILE A 126 " pdb=" CG2 ILE A 126 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.68e-01 ... (remaining 689 not shown) Planarity restraints: 740 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 80 " -0.041 5.00e-02 4.00e+02 6.11e-02 5.98e+00 pdb=" N PRO A 81 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO A 81 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 81 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 326 " 0.039 5.00e-02 4.00e+02 5.87e-02 5.51e+00 pdb=" N PRO A 327 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 327 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 327 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 286 " -0.038 5.00e-02 4.00e+02 5.61e-02 5.04e+00 pdb=" N PRO A 287 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 287 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 287 " -0.032 5.00e-02 4.00e+02 ... (remaining 737 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 1415 2.84 - 3.36: 3748 3.36 - 3.87: 7189 3.87 - 4.39: 8184 4.39 - 4.90: 14266 Nonbonded interactions: 34802 Sorted by model distance: nonbonded pdb=" O LEU A 74 " pdb=" OG1 THR A 78 " model vdw 2.331 2.440 nonbonded pdb=" O ALA B 23 " pdb=" OG SER B 26 " model vdw 2.353 2.440 nonbonded pdb=" O SER D 83 " pdb=" OG SER D 83 " model vdw 2.369 2.440 nonbonded pdb=" NH2 ARG A 124 " pdb=" OG SER A 329 " model vdw 2.384 2.520 nonbonded pdb=" O GLN B 101 " pdb=" ND2 ASN B 105 " model vdw 2.396 2.520 ... (remaining 34797 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 Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.740 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 16.700 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 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:12.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 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 : 0.006 0.186 4391 Z= 0.451 Angle : 0.860 8.907 5989 Z= 0.462 Chirality : 0.051 0.192 692 Planarity : 0.007 0.061 740 Dihedral : 15.400 83.214 1489 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.62 (0.30), residues: 544 helix: -2.14 (0.24), residues: 271 sheet: -1.98 (0.50), residues: 100 loop : -2.68 (0.41), residues: 173 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.503 Fit side-chains outliers start: 0 outliers final: 1 residues processed: 74 average time/residue: 0.7823 time to fit residues: 61.1865 Evaluate side-chains 56 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 55 time to evaluate : 0.472 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.6417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 HIS B 112 ASN B 211 ASN ** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 103 HIS D 111 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4391 Z= 0.247 Angle : 0.561 5.608 5989 Z= 0.292 Chirality : 0.043 0.220 692 Planarity : 0.005 0.043 740 Dihedral : 7.914 73.089 621 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.33 % Allowed : 15.12 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.34), residues: 544 helix: -0.30 (0.29), residues: 277 sheet: -1.52 (0.51), residues: 100 loop : -2.12 (0.45), residues: 167 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 61 time to evaluate : 0.483 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 65 average time/residue: 0.8770 time to fit residues: 60.0996 Evaluate side-chains 62 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 57 time to evaluate : 0.488 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 2 residues processed: 3 average time/residue: 0.0937 time to fit residues: 1.0510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 0.0040 chunk 15 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 211 ASN B 226 ASN ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4391 Z= 0.231 Angle : 0.549 6.535 5989 Z= 0.283 Chirality : 0.042 0.139 692 Planarity : 0.004 0.043 740 Dihedral : 7.769 72.995 621 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.26 % Allowed : 17.44 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.36), residues: 544 helix: 0.38 (0.30), residues: 277 sheet: -1.26 (0.52), residues: 100 loop : -1.84 (0.47), residues: 167 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 65 time to evaluate : 0.482 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 5 residues processed: 74 average time/residue: 0.8314 time to fit residues: 64.8577 Evaluate side-chains 64 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 59 time to evaluate : 0.486 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 2 average time/residue: 0.0662 time to fit residues: 0.8568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 49 optimal weight: 0.1980 chunk 52 optimal weight: 0.2980 chunk 46 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 211 ASN D 31 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4391 Z= 0.175 Angle : 0.523 5.416 5989 Z= 0.269 Chirality : 0.041 0.147 692 Planarity : 0.004 0.039 740 Dihedral : 7.604 71.872 621 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.33 % Allowed : 18.84 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.36), residues: 544 helix: 0.80 (0.31), residues: 277 sheet: -1.12 (0.52), residues: 100 loop : -1.64 (0.47), residues: 167 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 62 time to evaluate : 0.483 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 70 average time/residue: 0.9152 time to fit residues: 67.2672 Evaluate side-chains 64 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 60 time to evaluate : 0.479 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 0.6528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 38 optimal weight: 0.4980 chunk 21 optimal weight: 1.9990 chunk 44 optimal weight: 0.4980 chunk 36 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 17 optimal weight: 0.4980 chunk 47 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 211 ASN D 31 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4391 Z= 0.191 Angle : 0.524 5.578 5989 Z= 0.268 Chirality : 0.041 0.133 692 Planarity : 0.004 0.039 740 Dihedral : 7.498 71.414 621 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.26 % Allowed : 18.60 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.37), residues: 544 helix: 0.95 (0.31), residues: 277 sheet: -1.04 (0.52), residues: 100 loop : -1.55 (0.48), residues: 167 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 58 time to evaluate : 0.506 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 67 average time/residue: 0.8945 time to fit residues: 63.1246 Evaluate side-chains 62 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 56 time to evaluate : 0.491 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 4 residues processed: 2 average time/residue: 0.0750 time to fit residues: 0.9030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 52 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 4 optimal weight: 0.0370 chunk 17 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 211 ASN D 31 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4391 Z= 0.186 Angle : 0.518 5.924 5989 Z= 0.264 Chirality : 0.041 0.136 692 Planarity : 0.004 0.037 740 Dihedral : 7.444 71.272 621 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.79 % Allowed : 19.07 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.37), residues: 544 helix: 1.09 (0.32), residues: 277 sheet: -0.92 (0.52), residues: 100 loop : -1.46 (0.48), residues: 167 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 58 time to evaluate : 0.486 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 67 average time/residue: 0.8717 time to fit residues: 61.4668 Evaluate side-chains 63 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 57 time to evaluate : 0.464 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 0.0934 time to fit residues: 0.7601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 52 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.3980 chunk 24 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 10 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 31 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4391 Z= 0.212 Angle : 0.531 6.452 5989 Z= 0.270 Chirality : 0.042 0.148 692 Planarity : 0.004 0.039 740 Dihedral : 7.373 71.666 621 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.09 % Allowed : 19.30 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.37), residues: 544 helix: 1.02 (0.32), residues: 281 sheet: -0.87 (0.52), residues: 100 loop : -1.33 (0.50), residues: 163 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 58 time to evaluate : 0.489 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 66 average time/residue: 0.9362 time to fit residues: 64.8958 Evaluate side-chains 63 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 57 time to evaluate : 0.487 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 0.0899 time to fit residues: 0.7847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 4 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 45 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 31 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4391 Z= 0.246 Angle : 0.541 5.892 5989 Z= 0.277 Chirality : 0.042 0.148 692 Planarity : 0.004 0.038 740 Dihedral : 7.417 71.501 621 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.33 % Allowed : 20.47 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.37), residues: 544 helix: 1.00 (0.32), residues: 281 sheet: -0.87 (0.52), residues: 100 loop : -1.34 (0.50), residues: 163 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 61 time to evaluate : 0.497 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 68 average time/residue: 0.9487 time to fit residues: 67.6771 Evaluate side-chains 67 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 61 time to evaluate : 0.492 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 4 residues processed: 2 average time/residue: 0.0632 time to fit residues: 0.8336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 31 optimal weight: 0.0870 chunk 51 optimal weight: 0.0870 chunk 24 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 53 optimal weight: 0.3980 chunk 49 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 overall best weight: 0.3536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN D 31 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4391 Z= 0.147 Angle : 0.495 5.181 5989 Z= 0.253 Chirality : 0.040 0.143 692 Planarity : 0.004 0.038 740 Dihedral : 7.247 70.237 621 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.63 % Allowed : 22.09 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.38), residues: 544 helix: 1.33 (0.32), residues: 280 sheet: -0.74 (0.52), residues: 101 loop : -1.29 (0.50), residues: 163 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 60 time to evaluate : 0.531 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 66 average time/residue: 0.8903 time to fit residues: 61.8559 Evaluate side-chains 65 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 59 time to evaluate : 0.484 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 2 average time/residue: 0.0896 time to fit residues: 0.9234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 0.0980 chunk 33 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 34 optimal weight: 0.2980 chunk 45 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 39 optimal weight: 0.5980 chunk 6 optimal weight: 0.2980 chunk 11 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 211 ASN D 31 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4391 Z= 0.157 Angle : 0.504 5.140 5989 Z= 0.258 Chirality : 0.041 0.182 692 Planarity : 0.004 0.036 740 Dihedral : 7.231 70.218 621 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.63 % Allowed : 22.33 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.38), residues: 544 helix: 1.35 (0.32), residues: 280 sheet: -0.70 (0.55), residues: 90 loop : -1.08 (0.48), residues: 174 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 60 time to evaluate : 0.529 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 66 average time/residue: 0.9276 time to fit residues: 64.3434 Evaluate side-chains 63 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 59 time to evaluate : 0.449 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 0.6708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 37 optimal weight: 0.1980 chunk 2 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 49 optimal weight: 0.0170 chunk 28 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.6020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 211 ASN D 31 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.172619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.132563 restraints weight = 4373.514| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.45 r_work: 0.3139 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4391 Z= 0.196 Angle : 0.536 7.137 5989 Z= 0.275 Chirality : 0.041 0.183 692 Planarity : 0.004 0.037 740 Dihedral : 7.273 70.641 621 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.40 % Allowed : 22.79 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.37), residues: 544 helix: 1.24 (0.32), residues: 280 sheet: -0.40 (0.55), residues: 97 loop : -1.30 (0.48), residues: 167 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1804.23 seconds wall clock time: 32 minutes 46.82 seconds (1966.82 seconds total)