Starting phenix.real_space_refine on Mon Nov 13 20:44:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wop_32654/11_2023/7wop_32654.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wop_32654/11_2023/7wop_32654.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wop_32654/11_2023/7wop_32654.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wop_32654/11_2023/7wop_32654.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wop_32654/11_2023/7wop_32654.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wop_32654/11_2023/7wop_32654.pdb" } resolution = 3.51 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.016 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 23 5.16 5 C 3212 2.51 5 N 863 2.21 5 O 1009 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 346": "NH1" <-> "NH2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 408": "NH1" <-> "NH2" Residue "A ARG 454": "NH1" <-> "NH2" Residue "A ARG 457": "NH1" <-> "NH2" Residue "A ARG 466": "NH1" <-> "NH2" Residue "B PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 197": "NH1" <-> "NH2" Residue "B ARG 223": "NH1" <-> "NH2" Residue "B TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 152": "NH1" <-> "NH2" Residue "C ARG 224": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 5107 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1588 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 185} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1754 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 225} Chain breaks: 1 Chain: "C" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1765 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Time building chain proxies: 3.41, per 1000 atoms: 0.67 Number of scatterers: 5107 At special positions: 0 Unit cell: (86.184, 78.736, 102.144, 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 23 16.00 O 1009 8.00 N 863 7.00 C 3212 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 90 " distance=2.03 Simple disulfide: pdb=" SG CYS B 148 " - pdb=" SG CYS B 221 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 89 " distance=2.03 Simple disulfide: pdb=" SG CYS C 146 " - pdb=" SG CYS C 220 " 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: 1.97 Conformation dependent library (CDL) restraints added in 1.0 seconds 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1190 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 10 sheets defined 5.5% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.655A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 removed outlier: 3.830A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.546A pdb=" N GLU A 406 " --> pdb=" O ARG A 403 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 84 removed outlier: 3.500A pdb=" N GLU C 84 " --> pdb=" O SER C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 156 removed outlier: 3.500A pdb=" N HIS C 156 " --> pdb=" O PHE C 153 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 356 through 358 Processing sheet with id=AA2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA3, first strand: chain 'B' and resid 48 through 50 removed outlier: 6.502A pdb=" N TRP B 37 " --> pdb=" O MET B 49 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR B 106 " --> pdb=" O TYR B 88 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 64 through 69 removed outlier: 5.110A pdb=" N SER B 65 " --> pdb=" O THR B 76 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER B 67 " --> pdb=" O SER B 74 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 172 through 177 removed outlier: 5.785A pdb=" N TRP B 173 " --> pdb=" O ARG B 164 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ARG B 164 " --> pdb=" O TRP B 173 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET B 160 " --> pdb=" O ILE B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 21 through 23 Processing sheet with id=AA7, first strand: chain 'C' and resid 46 through 49 removed outlier: 6.716A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASN C 97 " --> pdb=" O ASP C 93 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 46 through 49 removed outlier: 6.716A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR C 87 " --> pdb=" O THR C 104 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 143 through 144 Processing sheet with id=AB1, first strand: chain 'C' and resid 182 through 184 removed outlier: 3.696A pdb=" N TYR C 183 " --> pdb=" O VAL C 174 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N TRP C 160 " --> pdb=" O VAL C 172 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N VAL C 174 " --> pdb=" O MET C 158 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N MET C 158 " --> pdb=" O VAL C 174 " (cutoff:3.500A) 87 hydrogen bonds defined for protein. 195 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: 1.28 Time building geometry restraints manager: 2.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1663 1.35 - 1.46: 1355 1.46 - 1.58: 2187 1.58 - 1.70: 0 1.70 - 1.81: 30 Bond restraints: 5235 Sorted by residual: bond pdb=" N GLY C 237 " pdb=" CA GLY C 237 " ideal model delta sigma weight residual 1.458 1.447 0.011 9.20e-03 1.18e+04 1.34e+00 bond pdb=" CA PRO B 228 " pdb=" C PRO B 228 " ideal model delta sigma weight residual 1.526 1.518 0.008 8.50e-03 1.38e+04 8.29e-01 bond pdb=" C ILE B 226 " pdb=" O ILE B 226 " ideal model delta sigma weight residual 1.232 1.242 -0.010 1.15e-02 7.56e+03 7.95e-01 bond pdb=" CA GLY A 476 " pdb=" C GLY A 476 " ideal model delta sigma weight residual 1.514 1.527 -0.012 1.41e-02 5.03e+03 7.51e-01 bond pdb=" N THR B 19 " pdb=" CA THR B 19 " ideal model delta sigma weight residual 1.460 1.470 -0.011 1.42e-02 4.96e+03 5.62e-01 ... (remaining 5230 not shown) Histogram of bond angle deviations from ideal: 100.51 - 107.20: 166 107.20 - 113.89: 2745 113.89 - 120.58: 1949 120.58 - 127.27: 2199 127.27 - 133.97: 57 Bond angle restraints: 7116 Sorted by residual: angle pdb=" C SER C 51 " pdb=" N ASN C 52 " pdb=" CA ASN C 52 " ideal model delta sigma weight residual 121.54 127.03 -5.49 1.91e+00 2.74e-01 8.25e+00 angle pdb=" N ASN A 481 " pdb=" CA ASN A 481 " pdb=" C ASN A 481 " ideal model delta sigma weight residual 113.15 109.85 3.30 1.19e+00 7.06e-01 7.69e+00 angle pdb=" N GLY A 504 " pdb=" CA GLY A 504 " pdb=" C GLY A 504 " ideal model delta sigma weight residual 113.79 110.74 3.05 1.17e+00 7.31e-01 6.81e+00 angle pdb=" N GLY B 95 " pdb=" CA GLY B 95 " pdb=" C GLY B 95 " ideal model delta sigma weight residual 111.36 114.27 -2.91 1.17e+00 7.31e-01 6.17e+00 angle pdb=" N THR B 25 " pdb=" CA THR B 25 " pdb=" C THR B 25 " ideal model delta sigma weight residual 114.09 110.45 3.64 1.55e+00 4.16e-01 5.51e+00 ... (remaining 7111 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.21: 2847 16.21 - 32.42: 166 32.42 - 48.63: 36 48.63 - 64.84: 8 64.84 - 81.05: 4 Dihedral angle restraints: 3061 sinusoidal: 1163 harmonic: 1898 Sorted by residual: dihedral pdb=" CA CYS A 336 " pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " ideal model delta sinusoidal sigma weight residual 79.00 20.34 58.66 1 2.00e+01 2.50e-03 1.15e+01 dihedral pdb=" CA PRO B 228 " pdb=" C PRO B 228 " pdb=" N TYR B 229 " pdb=" CA TYR B 229 " ideal model delta harmonic sigma weight residual -180.00 -163.60 -16.40 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" N PHE B 193 " pdb=" CA PHE B 193 " pdb=" CB PHE B 193 " pdb=" CG PHE B 193 " ideal model delta sinusoidal sigma weight residual 180.00 -120.02 -59.98 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 3058 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 425 0.029 - 0.057: 221 0.057 - 0.086: 65 0.086 - 0.115: 36 0.115 - 0.143: 6 Chirality restraints: 753 Sorted by residual: chirality pdb=" CA VAL A 483 " pdb=" N VAL A 483 " pdb=" C VAL A 483 " pdb=" CB VAL A 483 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.14e-01 chirality pdb=" CB VAL A 433 " pdb=" CA VAL A 433 " pdb=" CG1 VAL A 433 " pdb=" CG2 VAL A 433 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.04e-01 chirality pdb=" CA ILE B 50 " pdb=" N ILE B 50 " pdb=" C ILE B 50 " pdb=" CB ILE B 50 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.89e-01 ... (remaining 750 not shown) Planarity restraints: 932 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 7 " -0.032 5.00e-02 4.00e+02 4.94e-02 3.91e+00 pdb=" N PRO B 8 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 8 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 8 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 166 " 0.032 5.00e-02 4.00e+02 4.84e-02 3.75e+00 pdb=" N PRO B 167 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 167 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 167 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C 6 " -0.030 5.00e-02 4.00e+02 4.61e-02 3.40e+00 pdb=" N PRO C 7 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO C 7 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 7 " -0.025 5.00e-02 4.00e+02 ... (remaining 929 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 413 2.74 - 3.28: 5253 3.28 - 3.82: 8454 3.82 - 4.36: 9662 4.36 - 4.90: 16798 Nonbonded interactions: 40580 Sorted by model distance: nonbonded pdb=" OG SER B 36 " pdb=" OG SER B 91 " model vdw 2.203 2.440 nonbonded pdb=" O THR C 33 " pdb=" OH TYR C 236 " model vdw 2.233 2.440 nonbonded pdb=" OG SER C 27 " pdb=" OD1 ASP C 94 " model vdw 2.235 2.440 nonbonded pdb=" O LEU A 455 " pdb=" OH TYR B 159 " model vdw 2.306 2.440 nonbonded pdb=" OG SER B 147 " pdb=" OG1 THR B 203 " model vdw 2.328 2.440 ... (remaining 40575 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.400 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: 6.660 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 18.840 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6451 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 : 0.002 0.037 5235 Z= 0.133 Angle : 0.536 5.738 7116 Z= 0.311 Chirality : 0.040 0.143 753 Planarity : 0.004 0.049 932 Dihedral : 10.828 81.052 1847 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.38 % Favored : 88.62 % Rotamer: Outliers : 9.21 % Allowed : 8.48 % Favored : 82.31 % 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: -4.81 (0.27), residues: 659 helix: -4.90 (0.33), residues: 26 sheet: -2.57 (0.38), residues: 157 loop : -3.60 (0.23), residues: 476 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 158 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 19 residues processed: 197 average time/residue: 0.1768 time to fit residues: 43.9137 Evaluate side-chains 159 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 140 time to evaluate : 0.561 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1218 time to fit residues: 3.8828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 54 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.0870 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN A 409 GLN ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 GLN ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 GLN ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 ASN B 202 ASN ** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 16 GLN C 39 GLN C 80 GLN C 97 ASN C 137 GLN ** C 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6661 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5235 Z= 0.281 Angle : 0.663 7.029 7116 Z= 0.344 Chirality : 0.045 0.216 753 Planarity : 0.005 0.051 932 Dihedral : 4.530 38.763 739 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 18.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.17 % Favored : 84.83 % Rotamer: Outliers : 4.69 % Allowed : 18.95 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.40 (0.28), residues: 659 helix: -4.17 (0.49), residues: 34 sheet: -1.77 (0.42), residues: 140 loop : -3.48 (0.24), residues: 485 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 158 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 15 residues processed: 173 average time/residue: 0.1679 time to fit residues: 37.6513 Evaluate side-chains 165 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 150 time to evaluate : 0.578 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.0551 time to fit residues: 2.2529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 32 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 59 optimal weight: 0.4980 chunk 63 optimal weight: 0.0770 chunk 52 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN A 360 ASN ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 16 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6679 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5235 Z= 0.259 Angle : 0.649 6.841 7116 Z= 0.335 Chirality : 0.046 0.157 753 Planarity : 0.005 0.050 932 Dihedral : 4.702 39.999 739 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 19.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.02 % Favored : 84.98 % Rotamer: Outliers : 3.79 % Allowed : 21.66 % Favored : 74.55 % 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: -4.21 (0.29), residues: 659 helix: -3.54 (0.64), residues: 33 sheet: -1.90 (0.41), residues: 153 loop : -3.32 (0.25), residues: 473 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 145 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 9 residues processed: 157 average time/residue: 0.1817 time to fit residues: 36.7965 Evaluate side-chains 155 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 146 time to evaluate : 0.604 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0631 time to fit residues: 1.9406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 58 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 30 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 28 optimal weight: 0.3980 chunk 39 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 31 optimal weight: 0.1980 chunk 56 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 ASN C 32 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6712 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5235 Z= 0.269 Angle : 0.663 6.409 7116 Z= 0.344 Chirality : 0.046 0.150 753 Planarity : 0.005 0.045 932 Dihedral : 4.969 41.252 739 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 20.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.54 % Favored : 83.46 % Rotamer: Outliers : 3.25 % Allowed : 22.92 % Favored : 73.83 % 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: -4.15 (0.29), residues: 659 helix: -4.02 (0.67), residues: 28 sheet: -2.02 (0.37), residues: 174 loop : -3.20 (0.26), residues: 457 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 144 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 12 residues processed: 155 average time/residue: 0.1698 time to fit residues: 33.8998 Evaluate side-chains 156 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 144 time to evaluate : 0.537 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0616 time to fit residues: 2.1250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 52 optimal weight: 0.0670 chunk 35 optimal weight: 0.1980 chunk 0 optimal weight: 2.9990 chunk 46 optimal weight: 0.0670 chunk 25 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 21 optimal weight: 7.9990 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6686 moved from start: 0.3751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5235 Z= 0.220 Angle : 0.643 5.892 7116 Z= 0.333 Chirality : 0.045 0.146 753 Planarity : 0.005 0.044 932 Dihedral : 4.895 42.718 739 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 19.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.33 % Favored : 84.67 % Rotamer: Outliers : 3.43 % Allowed : 23.29 % Favored : 73.29 % 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: -3.98 (0.30), residues: 659 helix: -3.25 (0.68), residues: 41 sheet: -1.92 (0.39), residues: 166 loop : -3.08 (0.27), residues: 452 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 145 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 9 residues processed: 156 average time/residue: 0.1678 time to fit residues: 33.8190 Evaluate side-chains 151 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 142 time to evaluate : 0.571 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0532 time to fit residues: 1.6489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 56 optimal weight: 2.9990 chunk 12 optimal weight: 0.0010 chunk 36 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6740 moved from start: 0.4098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5235 Z= 0.289 Angle : 0.678 5.714 7116 Z= 0.355 Chirality : 0.047 0.184 753 Planarity : 0.005 0.045 932 Dihedral : 5.159 42.582 739 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 21.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.06 % Favored : 81.94 % Rotamer: Outliers : 2.35 % Allowed : 25.81 % Favored : 71.84 % 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: -3.98 (0.30), residues: 659 helix: -3.02 (0.78), residues: 34 sheet: -1.70 (0.39), residues: 165 loop : -3.22 (0.26), residues: 460 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 144 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 6 residues processed: 149 average time/residue: 0.1764 time to fit residues: 33.5004 Evaluate side-chains 149 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 143 time to evaluate : 0.533 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0576 time to fit residues: 1.3277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 7 optimal weight: 0.3980 chunk 35 optimal weight: 0.4980 chunk 45 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 38 optimal weight: 0.4980 chunk 28 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6724 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 5235 Z= 0.253 Angle : 0.687 8.800 7116 Z= 0.358 Chirality : 0.047 0.178 753 Planarity : 0.005 0.045 932 Dihedral : 5.103 42.966 739 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 20.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.84 % Favored : 83.16 % Rotamer: Outliers : 2.89 % Allowed : 25.63 % Favored : 71.48 % 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: -3.99 (0.30), residues: 659 helix: -3.22 (0.66), residues: 41 sheet: -1.67 (0.39), residues: 165 loop : -3.21 (0.26), residues: 453 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 141 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 5 residues processed: 150 average time/residue: 0.1816 time to fit residues: 34.8350 Evaluate side-chains 149 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 144 time to evaluate : 0.588 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0539 time to fit residues: 1.2253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 12 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 5 optimal weight: 0.3980 chunk 49 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 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 414 GLN ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6770 moved from start: 0.4584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 5235 Z= 0.328 Angle : 0.738 7.742 7116 Z= 0.387 Chirality : 0.048 0.184 753 Planarity : 0.005 0.045 932 Dihedral : 5.474 43.214 739 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 23.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.51 % Favored : 81.49 % Rotamer: Outliers : 2.53 % Allowed : 25.99 % Favored : 71.48 % 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: -4.03 (0.29), residues: 659 helix: -3.63 (0.71), residues: 28 sheet: -1.58 (0.41), residues: 151 loop : -3.26 (0.25), residues: 480 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 152 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 9 residues processed: 157 average time/residue: 0.1770 time to fit residues: 35.6800 Evaluate side-chains 160 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 151 time to evaluate : 0.574 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 9 average time/residue: 0.0600 time to fit residues: 1.7149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 25 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 chunk 37 optimal weight: 0.3980 chunk 29 optimal weight: 1.9990 chunk 42 optimal weight: 0.3980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6730 moved from start: 0.4703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 5235 Z= 0.256 Angle : 0.736 8.617 7116 Z= 0.386 Chirality : 0.048 0.248 753 Planarity : 0.005 0.045 932 Dihedral : 5.431 45.172 739 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 21.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.84 % Favored : 83.16 % Rotamer: Outliers : 1.26 % Allowed : 28.52 % Favored : 70.22 % 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: -3.94 (0.29), residues: 659 helix: -3.30 (0.80), residues: 28 sheet: -1.65 (0.41), residues: 158 loop : -3.17 (0.25), residues: 473 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 140 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 142 average time/residue: 0.1801 time to fit residues: 32.4643 Evaluate side-chains 141 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 136 time to evaluate : 0.511 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0561 time to fit residues: 1.2502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 64 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 chunk 51 optimal weight: 0.3980 chunk 5 optimal weight: 0.0980 chunk 39 optimal weight: 0.9980 chunk 31 optimal weight: 0.0670 chunk 40 optimal weight: 0.1980 chunk 54 optimal weight: 0.0570 chunk 15 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.1636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 GLN B 209 ASN ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 208 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6625 moved from start: 0.4707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5235 Z= 0.181 Angle : 0.706 8.081 7116 Z= 0.362 Chirality : 0.046 0.189 753 Planarity : 0.005 0.046 932 Dihedral : 5.016 45.624 739 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 17.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.57 % Favored : 85.43 % Rotamer: Outliers : 0.72 % Allowed : 29.96 % Favored : 69.31 % 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: -3.74 (0.30), residues: 659 helix: -3.08 (0.79), residues: 35 sheet: -1.57 (0.42), residues: 162 loop : -3.00 (0.26), residues: 462 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 141 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 142 average time/residue: 0.1597 time to fit residues: 29.6914 Evaluate side-chains 137 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 136 time to evaluate : 0.571 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0476 time to fit residues: 0.9005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 14 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 9 optimal weight: 0.4980 chunk 45 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 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 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 GLN ** 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 = 0.4003 r_free = 0.4003 target = 0.159855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.144526 restraints weight = 8240.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.148953 restraints weight = 4072.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.151734 restraints weight = 2349.687| |-----------------------------------------------------------------------------| r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6711 moved from start: 0.5005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 5235 Z= 0.334 Angle : 0.790 9.973 7116 Z= 0.411 Chirality : 0.049 0.217 753 Planarity : 0.005 0.044 932 Dihedral : 5.470 44.536 739 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 24.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.51 % Favored : 81.49 % Rotamer: Outliers : 0.72 % Allowed : 31.23 % Favored : 68.05 % 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: -3.82 (0.30), residues: 659 helix: -3.00 (0.86), residues: 28 sheet: -1.69 (0.41), residues: 160 loop : -3.05 (0.26), residues: 471 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1699.28 seconds wall clock time: 31 minutes 20.99 seconds (1880.99 seconds total)