Starting phenix.real_space_refine (version: 1.21rc1) on Tue Oct 3 00:07:26 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ont_17000/10_2023/8ont_17000_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ont_17000/10_2023/8ont_17000.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ont_17000/10_2023/8ont_17000.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ont_17000/10_2023/8ont_17000.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ont_17000/10_2023/8ont_17000_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ont_17000/10_2023/8ont_17000_trim_updated.pdb" } resolution = 3.66 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= 0.063 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 26 5.16 5 C 2831 2.51 5 N 696 2.21 5 O 762 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 120": "OE1" <-> "OE2" 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: 4316 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3367 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 16, 'TRANS': 421} Chain breaks: 1 Chain: "B" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 906 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {'PLC': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 2.93, per 1000 atoms: 0.68 Number of scatterers: 4316 At special positions: 0 Unit cell: (75.516, 96.348, 78.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 26 16.00 P 1 15.00 O 762 8.00 N 696 7.00 C 2831 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 298 " - pdb=" SG CYS A 311 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " 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: 1.74 Conformation dependent library (CDL) restraints added in 573.4 milliseconds 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1034 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 20 helices and 2 sheets defined 64.3% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 60 through 64 Processing helix chain 'A' and resid 67 through 80 Processing helix chain 'A' and resid 85 through 109 Processing helix chain 'A' and resid 113 through 119 Processing helix chain 'A' and resid 123 through 156 Proline residue: A 143 - end of helix Processing helix chain 'A' and resid 160 through 180 removed outlier: 4.672A pdb=" N LEU A 172 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU A 173 " --> pdb=" O PHE A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 207 Processing helix chain 'A' and resid 211 through 218 Processing helix chain 'A' and resid 226 through 240 Processing helix chain 'A' and resid 242 through 252 removed outlier: 4.231A pdb=" N SER A 249 " --> pdb=" O PHE A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 299 Processing helix chain 'A' and resid 305 through 313 removed outlier: 3.916A pdb=" N ASP A 313 " --> pdb=" O ASN A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 327 removed outlier: 3.792A pdb=" N ARG A 324 " --> pdb=" O MET A 321 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ASN A 325 " --> pdb=" O LEU A 322 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU A 327 " --> pdb=" O ARG A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 361 removed outlier: 3.972A pdb=" N PHE A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 389 Proline residue: A 382 - end of helix Processing helix chain 'A' and resid 392 through 422 Proline residue: A 411 - end of helix Proline residue: A 416 - end of helix Processing helix chain 'A' and resid 424 through 427 No H-bonds generated for 'chain 'A' and resid 424 through 427' Processing helix chain 'A' and resid 434 through 465 removed outlier: 3.891A pdb=" N HIS A 465 " --> pdb=" O ASP A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 495 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 3 through 7 Processing sheet with id= B, first strand: chain 'B' and resid 116 through 118 removed outlier: 3.943A pdb=" N ALA B 33 " --> pdb=" O GLY B 99 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N ARG B 38 " --> pdb=" O PHE B 47 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N PHE B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) 288 hydrogen bonds defined for protein. 822 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: 1.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 658 1.31 - 1.43: 1199 1.43 - 1.56: 2509 1.56 - 1.68: 2 1.68 - 1.81: 42 Bond restraints: 4410 Sorted by residual: bond pdb=" CB PLC A 601 " pdb=" O3 PLC A 601 " ideal model delta sigma weight residual 1.327 1.434 -0.107 2.00e-02 2.50e+03 2.85e+01 bond pdb=" C' PLC A 601 " pdb=" O2 PLC A 601 " ideal model delta sigma weight residual 1.332 1.430 -0.098 2.00e-02 2.50e+03 2.40e+01 bond pdb=" C' PLC A 601 " pdb=" C1' PLC A 601 " ideal model delta sigma weight residual 1.503 1.569 -0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" O3P PLC A 601 " pdb=" P PLC A 601 " ideal model delta sigma weight residual 1.634 1.689 -0.055 2.00e-02 2.50e+03 7.50e+00 bond pdb=" CB PLC A 601 " pdb=" C1B PLC A 601 " ideal model delta sigma weight residual 1.504 1.556 -0.052 2.00e-02 2.50e+03 6.70e+00 ... (remaining 4405 not shown) Histogram of bond angle deviations from ideal: 99.87 - 106.69: 108 106.69 - 113.51: 2520 113.51 - 120.33: 1659 120.33 - 127.15: 1664 127.15 - 133.97: 45 Bond angle restraints: 5996 Sorted by residual: angle pdb=" O3P PLC A 601 " pdb=" P PLC A 601 " pdb=" O4P PLC A 601 " ideal model delta sigma weight residual 93.62 109.58 -15.96 3.00e+00 1.11e-01 2.83e+01 angle pdb=" O1P PLC A 601 " pdb=" P PLC A 601 " pdb=" O2P PLC A 601 " ideal model delta sigma weight residual 119.61 109.11 10.50 3.00e+00 1.11e-01 1.22e+01 angle pdb=" C1' PLC A 601 " pdb=" C' PLC A 601 " pdb=" O2 PLC A 601 " ideal model delta sigma weight residual 111.19 119.79 -8.60 3.00e+00 1.11e-01 8.22e+00 angle pdb=" C1B PLC A 601 " pdb=" CB PLC A 601 " pdb=" O3 PLC A 601 " ideal model delta sigma weight residual 111.34 119.59 -8.25 3.00e+00 1.11e-01 7.57e+00 angle pdb=" C ALA A 300 " pdb=" CA ALA A 300 " pdb=" CB ALA A 300 " ideal model delta sigma weight residual 110.42 115.43 -5.01 1.99e+00 2.53e-01 6.34e+00 ... (remaining 5991 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.92: 2218 16.92 - 33.83: 272 33.83 - 50.75: 73 50.75 - 67.67: 11 67.67 - 84.58: 6 Dihedral angle restraints: 2580 sinusoidal: 972 harmonic: 1608 Sorted by residual: dihedral pdb=" C1B PLC A 601 " pdb=" CB PLC A 601 " pdb=" O3 PLC A 601 " pdb=" C3 PLC A 601 " ideal model delta sinusoidal sigma weight residual -178.77 -94.25 -84.52 1 3.00e+01 1.11e-03 9.65e+00 dihedral pdb=" CA ARG A 376 " pdb=" CB ARG A 376 " pdb=" CG ARG A 376 " pdb=" CD ARG A 376 " ideal model delta sinusoidal sigma weight residual 60.00 119.15 -59.15 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N GLN B 43 " pdb=" CA GLN B 43 " pdb=" CB GLN B 43 " pdb=" CG GLN B 43 " ideal model delta sinusoidal sigma weight residual -60.00 -118.74 58.74 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 2577 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 576 0.046 - 0.093: 114 0.093 - 0.139: 20 0.139 - 0.185: 0 0.185 - 0.231: 1 Chirality restraints: 711 Sorted by residual: chirality pdb=" C2 PLC A 601 " pdb=" C1 PLC A 601 " pdb=" C3 PLC A 601 " pdb=" O2 PLC A 601 " both_signs ideal model delta sigma weight residual False -2.31 -2.54 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA PRO A 143 " pdb=" N PRO A 143 " pdb=" C PRO A 143 " pdb=" CB PRO A 143 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.00e-01 chirality pdb=" CA VAL B 93 " pdb=" N VAL B 93 " pdb=" C VAL B 93 " pdb=" CB VAL B 93 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.69e-01 ... (remaining 708 not shown) Planarity restraints: 733 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 19 " -0.307 9.50e-02 1.11e+02 1.38e-01 1.17e+01 pdb=" NE ARG B 19 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG B 19 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG B 19 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 19 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN B 87 " 0.022 5.00e-02 4.00e+02 3.38e-02 1.83e+00 pdb=" N PRO B 88 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO B 88 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 88 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 142 " -0.022 5.00e-02 4.00e+02 3.31e-02 1.75e+00 pdb=" N PRO A 143 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 143 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 143 " -0.019 5.00e-02 4.00e+02 ... (remaining 730 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 29 2.51 - 3.10: 3532 3.10 - 3.70: 6596 3.70 - 4.30: 8978 4.30 - 4.90: 15787 Nonbonded interactions: 34922 Sorted by model distance: nonbonded pdb=" OH TYR A 82 " pdb=" OG1 THR A 296 " model vdw 1.908 2.440 nonbonded pdb=" O SER A 139 " pdb=" OG SER A 402 " model vdw 2.025 2.440 nonbonded pdb=" O VAL A 491 " pdb=" OG1 THR A 495 " model vdw 2.071 2.440 nonbonded pdb=" OD1 ASP A 66 " pdb=" OG1 THR A 346 " model vdw 2.076 2.440 nonbonded pdb=" OG1 THR A 351 " pdb=" ND2 ASN A 372 " model vdw 2.083 2.520 ... (remaining 34917 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: 0.250 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: 1.510 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 16.230 Find NCS groups from input model: 0.100 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.107 4410 Z= 0.384 Angle : 0.671 15.964 5996 Z= 0.314 Chirality : 0.038 0.231 711 Planarity : 0.006 0.138 733 Dihedral : 16.009 84.585 1540 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 33.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 0.87 % Allowed : 25.22 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.38), residues: 552 helix: 2.54 (0.27), residues: 360 sheet: -0.03 (0.82), residues: 47 loop : -2.54 (0.50), residues: 145 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 51 time to evaluate : 0.570 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 54 average time/residue: 0.2409 time to fit residues: 15.7362 Evaluate side-chains 54 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 51 time to evaluate : 0.478 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.0612 time to fit residues: 0.9645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 46 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 28 optimal weight: 0.0570 chunk 22 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 299 ASN ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 ASN A 473 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.1048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4410 Z= 0.229 Angle : 0.548 5.862 5996 Z= 0.276 Chirality : 0.039 0.131 711 Planarity : 0.004 0.044 733 Dihedral : 6.024 51.228 619 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 1.96 % Allowed : 23.04 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.38), residues: 552 helix: 2.74 (0.26), residues: 362 sheet: -0.11 (0.79), residues: 49 loop : -2.25 (0.54), residues: 141 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 59 time to evaluate : 0.444 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 65 average time/residue: 0.1864 time to fit residues: 15.2285 Evaluate side-chains 58 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 51 time to evaluate : 0.454 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 7 average time/residue: 0.0561 time to fit residues: 1.3256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 27 optimal weight: 0.9990 chunk 15 optimal weight: 0.0980 chunk 41 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4410 Z= 0.230 Angle : 0.520 5.962 5996 Z= 0.262 Chirality : 0.038 0.131 711 Planarity : 0.004 0.055 733 Dihedral : 5.867 51.316 619 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 3.04 % Allowed : 24.35 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.38), residues: 552 helix: 2.74 (0.26), residues: 355 sheet: -0.02 (0.78), residues: 49 loop : -1.94 (0.55), residues: 148 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 52 time to evaluate : 0.447 Fit side-chains outliers start: 14 outliers final: 7 residues processed: 63 average time/residue: 0.2065 time to fit residues: 16.2484 Evaluate side-chains 57 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 50 time to evaluate : 0.489 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0503 time to fit residues: 1.2829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 49 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 23 optimal weight: 0.0970 chunk 33 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 14 optimal weight: 0.4980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 372 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4410 Z= 0.194 Angle : 0.500 6.211 5996 Z= 0.252 Chirality : 0.037 0.132 711 Planarity : 0.004 0.056 733 Dihedral : 5.750 56.205 619 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 1.96 % Allowed : 23.91 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.38), residues: 552 helix: 2.62 (0.27), residues: 362 sheet: 0.43 (0.80), residues: 47 loop : -2.23 (0.53), residues: 143 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 52 time to evaluate : 0.400 Fit side-chains outliers start: 9 outliers final: 3 residues processed: 57 average time/residue: 0.1836 time to fit residues: 13.3420 Evaluate side-chains 52 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 49 time to evaluate : 0.449 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0543 time to fit residues: 0.8713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 44 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 4410 Z= 0.291 Angle : 0.543 6.055 5996 Z= 0.275 Chirality : 0.039 0.132 711 Planarity : 0.005 0.057 733 Dihedral : 5.920 59.610 619 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.04 % Allowed : 24.13 % Favored : 72.83 % 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: 1.56 (0.37), residues: 552 helix: 2.35 (0.27), residues: 362 sheet: 0.25 (0.81), residues: 49 loop : -2.36 (0.53), residues: 141 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 53 time to evaluate : 0.453 Fit side-chains outliers start: 14 outliers final: 8 residues processed: 63 average time/residue: 0.1874 time to fit residues: 14.8129 Evaluate side-chains 60 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 52 time to evaluate : 0.478 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1069 time to fit residues: 1.8051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 47 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4410 Z= 0.228 Angle : 0.532 9.891 5996 Z= 0.263 Chirality : 0.038 0.136 711 Planarity : 0.004 0.056 733 Dihedral : 5.855 55.756 619 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 1.09 % Allowed : 25.00 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.37), residues: 552 helix: 2.34 (0.27), residues: 362 sheet: 0.43 (0.81), residues: 49 loop : -2.42 (0.52), residues: 141 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 51 time to evaluate : 0.461 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 54 average time/residue: 0.1977 time to fit residues: 13.4522 Evaluate side-chains 49 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 48 time to evaluate : 0.449 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0619 time to fit residues: 0.6916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 5 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 44 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 33 optimal weight: 0.0870 chunk 32 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4410 Z= 0.212 Angle : 0.516 8.532 5996 Z= 0.256 Chirality : 0.038 0.136 711 Planarity : 0.004 0.057 733 Dihedral : 5.796 52.149 619 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 0.65 % Allowed : 26.52 % Favored : 72.83 % 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: 1.63 (0.37), residues: 552 helix: 2.36 (0.27), residues: 362 sheet: 0.83 (0.82), residues: 47 loop : -2.38 (0.51), residues: 143 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 49 time to evaluate : 0.497 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 52 average time/residue: 0.2141 time to fit residues: 13.9093 Evaluate side-chains 46 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.470 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 15 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 33 optimal weight: 0.0980 chunk 36 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 48 optimal weight: 0.4980 chunk 50 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4410 Z= 0.195 Angle : 0.499 8.357 5996 Z= 0.247 Chirality : 0.037 0.139 711 Planarity : 0.004 0.058 733 Dihedral : 5.756 55.927 619 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 0.65 % Allowed : 27.17 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.37), residues: 552 helix: 2.41 (0.27), residues: 362 sheet: 1.00 (0.82), residues: 47 loop : -2.36 (0.51), residues: 143 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 47 time to evaluate : 0.467 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 50 average time/residue: 0.2128 time to fit residues: 13.2533 Evaluate side-chains 48 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 47 time to evaluate : 0.452 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0725 time to fit residues: 0.7543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 50 optimal weight: 2.9990 chunk 29 optimal weight: 0.0370 chunk 21 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 15 optimal weight: 0.4980 chunk 44 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 chunk 52 optimal weight: 0.9980 chunk 31 optimal weight: 0.3980 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4410 Z= 0.182 Angle : 0.500 8.160 5996 Z= 0.246 Chirality : 0.037 0.143 711 Planarity : 0.004 0.058 733 Dihedral : 5.596 54.674 619 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.22 % Allowed : 27.17 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.37), residues: 552 helix: 2.46 (0.27), residues: 362 sheet: 1.07 (0.83), residues: 47 loop : -2.33 (0.51), residues: 143 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 47 time to evaluate : 0.495 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 48 average time/residue: 0.2167 time to fit residues: 12.9339 Evaluate side-chains 48 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 47 time to evaluate : 0.451 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0446 time to fit residues: 0.7040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 24 optimal weight: 3.9990 chunk 36 optimal weight: 0.3980 chunk 54 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4410 Z= 0.217 Angle : 0.514 8.057 5996 Z= 0.254 Chirality : 0.037 0.141 711 Planarity : 0.004 0.058 733 Dihedral : 5.324 44.645 619 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.00 % Allowed : 27.39 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.37), residues: 552 helix: 2.38 (0.27), residues: 362 sheet: 1.09 (0.82), residues: 47 loop : -2.35 (0.51), residues: 143 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.484 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.2105 time to fit residues: 11.8714 Evaluate side-chains 45 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.448 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 40 optimal weight: 5.9990 chunk 6 optimal weight: 0.4980 chunk 12 optimal weight: 1.9990 chunk 43 optimal weight: 0.3980 chunk 18 optimal weight: 0.7980 chunk 44 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 chunk 8 optimal weight: 0.4980 chunk 38 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.178248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.151598 restraints weight = 4362.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.146907 restraints weight = 5878.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.147142 restraints weight = 5931.369| |-----------------------------------------------------------------------------| r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4410 Z= 0.184 Angle : 0.501 8.002 5996 Z= 0.247 Chirality : 0.037 0.144 711 Planarity : 0.004 0.057 733 Dihedral : 5.022 42.469 619 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.00 % Allowed : 27.39 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.37), residues: 552 helix: 2.46 (0.27), residues: 362 sheet: 0.88 (0.81), residues: 49 loop : -2.36 (0.51), residues: 141 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1096.27 seconds wall clock time: 20 minutes 31.99 seconds (1231.99 seconds total)