Starting phenix.real_space_refine (version: 1.21rc1) on Tue Oct 3 00:28:12 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bvt_16271/10_2023/8bvt_16271_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bvt_16271/10_2023/8bvt_16271.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bvt_16271/10_2023/8bvt_16271_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bvt_16271/10_2023/8bvt_16271_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bvt_16271/10_2023/8bvt_16271_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bvt_16271/10_2023/8bvt_16271.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bvt_16271/10_2023/8bvt_16271.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bvt_16271/10_2023/8bvt_16271_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bvt_16271/10_2023/8bvt_16271_updated.pdb" } resolution = 3.94 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= 0.002 sd= 0.042 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 33 5.16 5 C 2907 2.51 5 N 776 2.21 5 O 801 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 359": "OD1" <-> "OD2" Residue "A TYR 482": "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: 4517 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 3933 Classifications: {'peptide': 508} Link IDs: {'PTRANS': 28, 'TRANS': 479} Chain breaks: 2 Chain: "B" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 565 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 3, 'TRANS': 111} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 353 Unresolved non-hydrogen angles: 462 Unresolved non-hydrogen dihedrals: 309 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'TYR:plan': 7, 'ASN:plan1': 3, 'TRP:plan': 5, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 216 Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'RTO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.86, per 1000 atoms: 0.63 Number of scatterers: 4517 At special positions: 0 Unit cell: (115.648, 70.72, 82.368, 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 33 16.00 O 801 8.00 N 776 7.00 C 2907 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 105 " distance=2.03 Simple disulfide: pdb=" SG CYS A 78 " - pdb=" SG CYS A 128 " 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: 1.86 Conformation dependent library (CDL) restraints added in 1.1 seconds 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1146 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 23 helices and 2 sheets defined 57.0% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 3 through 10 Processing helix chain 'A' and resid 15 through 41 removed outlier: 4.283A pdb=" N VAL A 21 " --> pdb=" O GLN A 17 " (cutoff:3.500A) Proline residue: A 27 - end of helix removed outlier: 4.747A pdb=" N LEU A 30 " --> pdb=" O ALA A 26 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLN A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ASN A 39 " --> pdb=" O ASN A 35 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N PHE A 40 " --> pdb=" O THR A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 124 Processing helix chain 'A' and resid 133 through 159 removed outlier: 3.687A pdb=" N GLN A 138 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY A 153 " --> pdb=" O ALA A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 180 Processing helix chain 'A' and resid 185 through 213 removed outlier: 3.746A pdb=" N SER A 201 " --> pdb=" O MET A 197 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N MET A 207 " --> pdb=" O ALA A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 243 removed outlier: 4.066A pdb=" N ARG A 219 " --> pdb=" O ILE A 216 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N ALA A 220 " --> pdb=" O HIS A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 267 Proline residue: A 257 - end of helix removed outlier: 4.009A pdb=" N ILE A 263 " --> pdb=" O PHE A 259 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N TYR A 264 " --> pdb=" O ILE A 260 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N PHE A 267 " --> pdb=" O ILE A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 278 Processing helix chain 'A' and resid 282 through 295 Processing helix chain 'A' and resid 299 through 302 No H-bonds generated for 'chain 'A' and resid 299 through 302' Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 327 through 331 Processing helix chain 'A' and resid 333 through 358 Processing helix chain 'A' and resid 361 through 363 No H-bonds generated for 'chain 'A' and resid 361 through 363' Processing helix chain 'A' and resid 367 through 391 removed outlier: 3.733A pdb=" N ASP A 378 " --> pdb=" O PHE A 374 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LEU A 379 " --> pdb=" O GLY A 375 " (cutoff:3.500A) Proline residue: A 380 - end of helix Processing helix chain 'A' and resid 395 through 414 Processing helix chain 'A' and resid 421 through 448 Processing helix chain 'A' and resid 454 through 477 Proline residue: A 473 - end of helix Processing helix chain 'A' and resid 485 through 501 Proline residue: A 494 - end of helix Processing helix chain 'A' and resid 516 through 522 removed outlier: 3.757A pdb=" N LEU A 519 " --> pdb=" O VAL A 516 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LYS A 520 " --> pdb=" O GLN A 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 55 No H-bonds generated for 'chain 'B' and resid 53 through 55' Processing helix chain 'B' and resid 88 through 90 No H-bonds generated for 'chain 'B' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'B' and resid 4 through 7 removed outlier: 3.802A pdb=" N LEU B 18 " --> pdb=" O MET B 83 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET B 83 " --> pdb=" O LEU B 18 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N CYS B 22 " --> pdb=" O VAL B 79 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL B 79 " --> pdb=" O CYS B 22 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 93 through 96 removed outlier: 3.566A pdb=" N ALA B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) 250 hydrogen bonds defined for protein. 669 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: 1.19 Time building geometry restraints manager: 2.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.01 - 1.17: 1 1.17 - 1.33: 1150 1.33 - 1.49: 1534 1.49 - 1.66: 1875 1.66 - 1.82: 53 Bond restraints: 4613 Sorted by residual: bond pdb=" CB PRO A 88 " pdb=" CG PRO A 88 " ideal model delta sigma weight residual 1.492 1.011 0.481 5.00e-02 4.00e+02 9.25e+01 bond pdb=" CG PRO A 88 " pdb=" CD PRO A 88 " ideal model delta sigma weight residual 1.503 1.217 0.286 3.40e-02 8.65e+02 7.06e+01 bond pdb=" N PRO A 88 " pdb=" CA PRO A 88 " ideal model delta sigma weight residual 1.465 1.566 -0.101 2.03e-02 2.43e+03 2.49e+01 bond pdb=" CG PRO A 494 " pdb=" CD PRO A 494 " ideal model delta sigma weight residual 1.503 1.561 -0.058 3.40e-02 8.65e+02 2.91e+00 bond pdb=" CB PRO A 494 " pdb=" CG PRO A 494 " ideal model delta sigma weight residual 1.492 1.573 -0.081 5.00e-02 4.00e+02 2.60e+00 ... (remaining 4608 not shown) Histogram of bond angle deviations from ideal: 66.53 - 83.12: 2 83.12 - 99.70: 2 99.70 - 116.29: 3018 116.29 - 132.88: 3258 132.88 - 149.47: 12 Bond angle restraints: 6292 Sorted by residual: angle pdb=" CA PRO A 88 " pdb=" CB PRO A 88 " pdb=" CG PRO A 88 " ideal model delta sigma weight residual 104.50 66.53 37.97 1.90e+00 2.77e-01 3.99e+02 angle pdb=" N PRO A 88 " pdb=" CD PRO A 88 " pdb=" CG PRO A 88 " ideal model delta sigma weight residual 103.20 74.08 29.12 1.50e+00 4.44e-01 3.77e+02 angle pdb=" CB PRO A 88 " pdb=" CG PRO A 88 " pdb=" CD PRO A 88 " ideal model delta sigma weight residual 106.10 149.47 -43.37 3.20e+00 9.77e-02 1.84e+02 angle pdb=" CA PRO A 88 " pdb=" N PRO A 88 " pdb=" CD PRO A 88 " ideal model delta sigma weight residual 112.00 99.99 12.01 1.40e+00 5.10e-01 7.36e+01 angle pdb=" CA PRO A 494 " pdb=" N PRO A 494 " pdb=" CD PRO A 494 " ideal model delta sigma weight residual 112.00 102.70 9.30 1.40e+00 5.10e-01 4.41e+01 ... (remaining 6287 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 2316 17.69 - 35.37: 300 35.37 - 53.06: 73 53.06 - 70.75: 14 70.75 - 88.44: 10 Dihedral angle restraints: 2713 sinusoidal: 929 harmonic: 1784 Sorted by residual: dihedral pdb=" CB CYS A 78 " pdb=" SG CYS A 78 " pdb=" SG CYS A 128 " pdb=" CB CYS A 128 " ideal model delta sinusoidal sigma weight residual 93.00 27.55 65.45 1 1.00e+01 1.00e-02 5.61e+01 dihedral pdb=" N PRO A 88 " pdb=" CG PRO A 88 " pdb=" CD PRO A 88 " pdb=" CB PRO A 88 " ideal model delta sinusoidal sigma weight residual 30.00 107.54 -77.54 1 1.50e+01 4.44e-03 3.35e+01 dihedral pdb=" CA PRO A 88 " pdb=" CB PRO A 88 " pdb=" CG PRO A 88 " pdb=" CD PRO A 88 " ideal model delta sinusoidal sigma weight residual 38.00 123.96 -85.96 1 2.00e+01 2.50e-03 2.23e+01 ... (remaining 2710 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 564 0.048 - 0.095: 138 0.095 - 0.143: 31 0.143 - 0.190: 6 0.190 - 0.238: 3 Chirality restraints: 742 Sorted by residual: chirality pdb=" CA PRO A 494 " pdb=" N PRO A 494 " pdb=" C PRO A 494 " pdb=" CB PRO A 494 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA PRO A 88 " pdb=" N PRO A 88 " pdb=" C PRO A 88 " pdb=" CB PRO A 88 " both_signs ideal model delta sigma weight residual False 2.72 2.93 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA PRO A 257 " pdb=" N PRO A 257 " pdb=" C PRO A 257 " pdb=" CB PRO A 257 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 9.11e-01 ... (remaining 739 not shown) Planarity restraints: 799 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 114 " 0.052 2.00e-02 2.50e+03 9.66e-02 9.34e+01 pdb=" C SER B 114 " -0.167 2.00e-02 2.50e+03 pdb=" O SER B 114 " 0.061 2.00e-02 2.50e+03 pdb=" N ALA B 115 " 0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 493 " 0.070 5.00e-02 4.00e+02 1.00e-01 1.61e+01 pdb=" N PRO A 494 " -0.173 5.00e-02 4.00e+02 pdb=" CA PRO A 494 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO A 494 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 87 " 0.046 5.00e-02 4.00e+02 6.24e-02 6.23e+00 pdb=" N PRO A 88 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 88 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 88 " 0.035 5.00e-02 4.00e+02 ... (remaining 796 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 170 2.71 - 3.25: 4879 3.25 - 3.80: 7758 3.80 - 4.35: 8556 4.35 - 4.90: 14406 Nonbonded interactions: 35769 Sorted by model distance: nonbonded pdb=" OG1 THR A 172 " pdb=" OG SER A 198 " model vdw 2.157 2.440 nonbonded pdb=" OD1 ASP A 70 " pdb=" N GLN A 74 " model vdw 2.257 2.520 nonbonded pdb=" OG SER A 401 " pdb=" O CYS A 433 " model vdw 2.267 2.440 nonbonded pdb=" NH1 ARG A 394 " pdb=" OG1 THR A 507 " model vdw 2.276 2.520 nonbonded pdb=" ND2 ASN A 39 " pdb=" O MET A 358 " model vdw 2.285 2.520 ... (remaining 35764 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: 0.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.980 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 16.810 Find NCS groups from input model: 0.130 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 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 : 0.009 0.481 4613 Z= 0.380 Angle : 1.190 43.365 6292 Z= 0.569 Chirality : 0.046 0.238 742 Planarity : 0.007 0.100 799 Dihedral : 17.662 88.436 1561 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.23 % Allowed : 44.99 % Favored : 54.78 % 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: 0.33 (0.34), residues: 615 helix: 1.09 (0.27), residues: 357 sheet: 0.48 (0.82), residues: 48 loop : -1.34 (0.43), residues: 210 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 93 time to evaluate : 0.544 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 93 average time/residue: 0.1093 time to fit residues: 14.3480 Evaluate side-chains 92 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.591 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 50.0000 chunk 46 optimal weight: 6.9990 chunk 25 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 31 optimal weight: 0.0070 chunk 24 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 29 optimal weight: 9.9990 chunk 35 optimal weight: 0.8980 chunk 55 optimal weight: 20.0000 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.0506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4613 Z= 0.180 Angle : 0.708 12.880 6292 Z= 0.334 Chirality : 0.040 0.147 742 Planarity : 0.005 0.035 799 Dihedral : 4.873 59.756 671 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.03 % Allowed : 41.03 % Favored : 55.94 % 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: 0.42 (0.35), residues: 615 helix: 1.11 (0.28), residues: 357 sheet: 0.86 (0.84), residues: 47 loop : -1.27 (0.43), residues: 211 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 98 time to evaluate : 0.515 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 107 average time/residue: 0.1066 time to fit residues: 16.2285 Evaluate side-chains 103 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 95 time to evaluate : 0.533 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0461 time to fit residues: 1.3452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 30 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 55 optimal weight: 20.0000 chunk 59 optimal weight: 9.9990 chunk 49 optimal weight: 20.0000 chunk 18 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 54 optimal weight: 9.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.0714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4613 Z= 0.225 Angle : 0.662 9.661 6292 Z= 0.313 Chirality : 0.040 0.186 742 Planarity : 0.005 0.041 799 Dihedral : 4.642 57.133 671 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.80 % Allowed : 42.42 % Favored : 54.78 % 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: 0.43 (0.35), residues: 615 helix: 1.10 (0.28), residues: 357 sheet: 0.86 (0.83), residues: 48 loop : -1.24 (0.44), residues: 210 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 98 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 11 residues processed: 105 average time/residue: 0.1177 time to fit residues: 17.2065 Evaluate side-chains 107 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 96 time to evaluate : 0.539 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0530 time to fit residues: 1.6879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 41 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 6 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 37 optimal weight: 0.7980 chunk 55 optimal weight: 30.0000 chunk 58 optimal weight: 30.0000 chunk 29 optimal weight: 3.9990 chunk 52 optimal weight: 0.0060 chunk 15 optimal weight: 0.9980 chunk 49 optimal weight: 10.0000 overall best weight: 1.2798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.0922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4613 Z= 0.215 Angle : 0.682 11.845 6292 Z= 0.314 Chirality : 0.041 0.216 742 Planarity : 0.005 0.036 799 Dihedral : 4.578 55.806 671 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 4.66 % Allowed : 39.63 % Favored : 55.71 % 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: 0.38 (0.35), residues: 615 helix: 1.06 (0.28), residues: 357 sheet: 0.94 (0.82), residues: 48 loop : -1.30 (0.44), residues: 210 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 99 time to evaluate : 0.479 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 13 residues processed: 112 average time/residue: 0.1236 time to fit residues: 18.6000 Evaluate side-chains 110 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 97 time to evaluate : 0.452 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0487 time to fit residues: 1.7419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 50 optimal weight: 50.0000 chunk 40 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 52 optimal weight: 20.0000 chunk 14 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 53 optimal weight: 10.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 4613 Z= 0.291 Angle : 0.719 10.194 6292 Z= 0.338 Chirality : 0.042 0.177 742 Planarity : 0.005 0.039 799 Dihedral : 4.525 54.381 671 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 3.26 % Allowed : 40.33 % Favored : 56.41 % 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 (0.35), residues: 615 helix: 0.86 (0.28), residues: 359 sheet: 0.87 (0.80), residues: 51 loop : -1.25 (0.44), residues: 205 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 103 time to evaluate : 0.521 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 10 residues processed: 111 average time/residue: 0.1242 time to fit residues: 18.8663 Evaluate side-chains 106 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 96 time to evaluate : 0.468 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0533 time to fit residues: 1.6057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 59 optimal weight: 0.1980 chunk 48 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 56 optimal weight: 0.0970 chunk 6 optimal weight: 0.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 39 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4613 Z= 0.186 Angle : 0.727 11.641 6292 Z= 0.327 Chirality : 0.041 0.189 742 Planarity : 0.005 0.038 799 Dihedral : 4.453 54.520 671 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.40 % Allowed : 43.36 % Favored : 55.24 % 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: 0.27 (0.35), residues: 615 helix: 0.92 (0.28), residues: 358 sheet: 1.03 (0.81), residues: 50 loop : -1.31 (0.44), residues: 207 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 103 time to evaluate : 0.488 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 105 average time/residue: 0.1160 time to fit residues: 16.8390 Evaluate side-chains 97 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 93 time to evaluate : 0.506 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0457 time to fit residues: 1.0066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 49 optimal weight: 8.9990 chunk 32 optimal weight: 0.9990 chunk 58 optimal weight: 20.0000 chunk 36 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4613 Z= 0.226 Angle : 0.753 11.590 6292 Z= 0.338 Chirality : 0.041 0.173 742 Planarity : 0.005 0.039 799 Dihedral : 4.364 53.108 671 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.86 % Allowed : 43.12 % Favored : 55.01 % 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: 0.24 (0.35), residues: 615 helix: 0.87 (0.28), residues: 358 sheet: 1.03 (0.81), residues: 50 loop : -1.27 (0.44), residues: 207 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 97 time to evaluate : 0.512 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 101 average time/residue: 0.1138 time to fit residues: 16.2541 Evaluate side-chains 100 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 94 time to evaluate : 0.476 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0496 time to fit residues: 1.1452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 40 optimal weight: 0.3980 chunk 29 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 46 optimal weight: 0.0070 chunk 53 optimal weight: 20.0000 chunk 56 optimal weight: 4.9990 chunk 51 optimal weight: 40.0000 chunk 54 optimal weight: 8.9990 chunk 32 optimal weight: 6.9990 overall best weight: 1.8802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4613 Z= 0.279 Angle : 0.791 11.534 6292 Z= 0.358 Chirality : 0.043 0.168 742 Planarity : 0.005 0.038 799 Dihedral : 4.407 53.007 671 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.63 % Allowed : 43.36 % Favored : 55.01 % 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: 0.22 (0.35), residues: 615 helix: 0.83 (0.28), residues: 358 sheet: 0.99 (0.81), residues: 50 loop : -1.22 (0.44), residues: 207 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 97 time to evaluate : 0.474 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 100 average time/residue: 0.1170 time to fit residues: 16.4228 Evaluate side-chains 102 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 96 time to evaluate : 0.513 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0574 time to fit residues: 1.2973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 23 optimal weight: 0.0970 chunk 43 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 51 optimal weight: 40.0000 chunk 54 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 57 optimal weight: 30.0000 chunk 27 optimal weight: 2.9990 chunk 40 optimal weight: 0.0670 chunk 60 optimal weight: 30.0000 overall best weight: 0.9518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4613 Z= 0.210 Angle : 0.803 12.115 6292 Z= 0.353 Chirality : 0.042 0.168 742 Planarity : 0.005 0.036 799 Dihedral : 4.335 51.521 671 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.70 % Allowed : 43.12 % Favored : 56.18 % 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: 0.22 (0.35), residues: 615 helix: 0.84 (0.27), residues: 358 sheet: 1.01 (0.82), residues: 50 loop : -1.26 (0.44), residues: 207 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 97 time to evaluate : 0.549 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 97 average time/residue: 0.1166 time to fit residues: 15.8716 Evaluate side-chains 99 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 96 time to evaluate : 0.538 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0546 time to fit residues: 1.0022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 55 optimal weight: 20.0000 chunk 48 optimal weight: 0.0270 chunk 5 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 chunk 29 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 51 optimal weight: 50.0000 chunk 14 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 overall best weight: 1.1642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4613 Z= 0.226 Angle : 0.809 12.166 6292 Z= 0.356 Chirality : 0.042 0.167 742 Planarity : 0.005 0.037 799 Dihedral : 4.265 49.951 671 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.47 % Allowed : 43.82 % Favored : 55.71 % 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: 0.17 (0.35), residues: 615 helix: 0.79 (0.27), residues: 358 sheet: 1.01 (0.82), residues: 50 loop : -1.25 (0.44), residues: 207 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 98 time to evaluate : 0.544 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 98 average time/residue: 0.1274 time to fit residues: 17.0668 Evaluate side-chains 97 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 95 time to evaluate : 0.534 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0545 time to fit residues: 0.8797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 48 optimal weight: 0.8980 chunk 20 optimal weight: 0.1980 chunk 49 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 35 optimal weight: 0.3980 chunk 55 optimal weight: 20.0000 chunk 32 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 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 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.133022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.106236 restraints weight = 13218.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.109517 restraints weight = 6761.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.111756 restraints weight = 4371.063| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4613 Z= 0.201 Angle : 0.815 12.211 6292 Z= 0.353 Chirality : 0.042 0.164 742 Planarity : 0.005 0.037 799 Dihedral : 4.055 41.152 671 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.93 % Allowed : 44.52 % Favored : 54.55 % 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: 0.18 (0.35), residues: 615 helix: 0.81 (0.28), residues: 358 sheet: 1.02 (0.82), residues: 50 loop : -1.27 (0.44), residues: 207 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1272.98 seconds wall clock time: 23 minutes 42.96 seconds (1422.96 seconds total)