Starting phenix.real_space_refine on Sun Mar 10 19:32:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ont_17000/03_2024/8ont_17000_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ont_17000/03_2024/8ont_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_17000/03_2024/8ont_17000.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ont_17000/03_2024/8ont_17000.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ont_17000/03_2024/8ont_17000_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ont_17000/03_2024/8ont_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-dev-5265/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: 3.10, per 1000 atoms: 0.72 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: 2.16 Conformation dependent library (CDL) restraints added in 713.8 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: 0.92 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: 1.28 Time building geometry restraints manager: 2.26 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 - 20.83: 2315 20.83 - 41.66: 234 41.66 - 62.48: 34 62.48 - 83.31: 5 83.31 - 104.14: 6 Dihedral angle restraints: 2594 sinusoidal: 986 harmonic: 1608 Sorted by residual: dihedral pdb=" O2 PLC A 601 " pdb=" C1 PLC A 601 " pdb=" C2 PLC A 601 " pdb=" O3P PLC A 601 " ideal model delta sinusoidal sigma weight residual -55.71 48.43 -104.14 1 3.00e+01 1.11e-03 1.33e+01 dihedral pdb=" C3 PLC A 601 " pdb=" C1 PLC A 601 " pdb=" C2 PLC A 601 " pdb=" O3P PLC A 601 " ideal model delta sinusoidal sigma weight residual 67.16 168.71 -101.55 1 3.00e+01 1.11e-03 1.28e+01 dihedral pdb=" C2' PLC A 601 " pdb=" C' PLC A 601 " pdb=" C1' PLC A 601 " pdb=" O2 PLC A 601 " ideal model delta sinusoidal sigma weight residual 169.53 79.09 90.44 1 3.00e+01 1.11e-03 1.07e+01 ... (remaining 2591 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: 0.460 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: 0.050 Set scattering table: 0.040 Process input model: 17.590 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.730 ------------------------------------------------------------------------------- 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 : 16.916 104.141 1554 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 86 HIS 0.003 0.001 HIS A 248 PHE 0.014 0.001 PHE A 236 TYR 0.017 0.002 TYR B 80 ARG 0.004 0.000 ARG B 82 *********************** 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 : 0.477 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 54 average time/residue: 0.2435 time to fit residues: 15.8384 Evaluate side-chains 54 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 51 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain B residue 6 GLU 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: 2.9990 chunk 28 optimal weight: 0.0570 chunk 22 optimal weight: 0.5980 chunk 43 optimal weight: 4.9990 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: 0.6698 ------------------------------------------------------------------------------- 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: 0.7542 moved from start: 0.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4410 Z= 0.234 Angle : 0.555 5.917 5996 Z= 0.279 Chirality : 0.039 0.133 711 Planarity : 0.004 0.045 733 Dihedral : 8.660 80.363 640 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.61 % Allowed : 23.04 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.38), residues: 552 helix: 2.73 (0.26), residues: 362 sheet: -0.12 (0.80), residues: 49 loop : -2.27 (0.54), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 369 HIS 0.003 0.001 HIS A 248 PHE 0.012 0.001 PHE A 361 TYR 0.014 0.001 TYR A 335 ARG 0.004 0.000 ARG A 111 *********************** 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 70 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 58 time to evaluate : 0.448 Fit side-chains REVERT: B 108 SER cc_start: 0.8759 (m) cc_final: 0.8518 (m) outliers start: 12 outliers final: 7 residues processed: 66 average time/residue: 0.1755 time to fit residues: 14.6232 Evaluate side-chains 60 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 53 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 6 GLU Chi-restraints excluded: chain B residue 83 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 27 optimal weight: 2.9990 chunk 15 optimal weight: 0.0980 chunk 41 optimal weight: 3.9990 chunk 34 optimal weight: 0.0980 chunk 13 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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: 0.7558 moved from start: 0.1251 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= 0.242 Angle : 0.523 5.874 5996 Z= 0.265 Chirality : 0.038 0.133 711 Planarity : 0.005 0.055 733 Dihedral : 7.909 69.226 636 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 5.00 % Allowed : 22.61 % Favored : 72.39 % 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: 1.90 (0.38), residues: 552 helix: 2.66 (0.26), residues: 356 sheet: -0.07 (0.79), residues: 49 loop : -2.00 (0.55), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 161 HIS 0.003 0.001 HIS A 248 PHE 0.008 0.001 PHE A 236 TYR 0.012 0.001 TYR A 459 ARG 0.003 0.000 ARG A 111 *********************** 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 81 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 58 time to evaluate : 0.471 Fit side-chains REVERT: A 69 ASN cc_start: 0.7717 (OUTLIER) cc_final: 0.7434 (m110) REVERT: B 108 SER cc_start: 0.8772 (m) cc_final: 0.8552 (m) outliers start: 23 outliers final: 15 residues processed: 75 average time/residue: 0.1852 time to fit residues: 17.3300 Evaluate side-chains 71 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 55 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 112 HIS Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 421 CYS Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 6 GLU Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 74 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 49 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 23 optimal weight: 0.1980 chunk 33 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 26 optimal weight: 0.0980 chunk 47 optimal weight: 0.0060 chunk 14 optimal weight: 0.6980 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.1516 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= 0.169 Angle : 0.489 6.184 5996 Z= 0.248 Chirality : 0.037 0.134 711 Planarity : 0.004 0.057 733 Dihedral : 7.518 63.398 636 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.83 % Allowed : 23.91 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.37), residues: 552 helix: 2.63 (0.26), residues: 362 sheet: 0.32 (0.80), residues: 47 loop : -2.20 (0.53), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 161 HIS 0.002 0.001 HIS A 248 PHE 0.009 0.001 PHE A 361 TYR 0.010 0.001 TYR A 335 ARG 0.003 0.000 ARG A 111 *********************** 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 66 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 53 time to evaluate : 0.454 Fit side-chains REVERT: B 108 SER cc_start: 0.8763 (m) cc_final: 0.8549 (m) outliers start: 13 outliers final: 9 residues processed: 62 average time/residue: 0.1871 time to fit residues: 14.7563 Evaluate side-chains 58 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 49 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 6 GLU Chi-restraints excluded: chain B residue 74 ASN 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: 2.9990 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 36 optimal weight: 0.2980 chunk 27 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.1542 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= 0.236 Angle : 0.510 6.204 5996 Z= 0.258 Chirality : 0.038 0.131 711 Planarity : 0.004 0.057 733 Dihedral : 7.312 58.937 636 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 5.43 % Allowed : 22.61 % Favored : 71.96 % 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 (0.38), residues: 552 helix: 2.49 (0.27), residues: 362 sheet: 0.15 (0.80), residues: 49 loop : -2.34 (0.53), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 161 HIS 0.003 0.001 HIS A 248 PHE 0.008 0.001 PHE A 236 TYR 0.010 0.001 TYR A 459 ARG 0.004 0.000 ARG A 111 *********************** 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 75 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 50 time to evaluate : 0.479 Fit side-chains REVERT: A 69 ASN cc_start: 0.7944 (OUTLIER) cc_final: 0.7496 (m110) REVERT: A 285 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7761 (mp) REVERT: A 430 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8143 (mm) REVERT: B 34 MET cc_start: 0.8369 (mtp) cc_final: 0.8133 (ttm) outliers start: 25 outliers final: 15 residues processed: 70 average time/residue: 0.1843 time to fit residues: 16.1979 Evaluate side-chains 67 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 49 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 112 HIS Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 6 GLU Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 74 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 47 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 44 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 51 optimal weight: 0.0040 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.1610 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= 0.217 Angle : 0.521 9.784 5996 Z= 0.257 Chirality : 0.038 0.132 711 Planarity : 0.004 0.057 733 Dihedral : 7.204 56.513 636 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 5.22 % Allowed : 22.39 % Favored : 72.39 % 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: 1.67 (0.37), residues: 552 helix: 2.44 (0.27), residues: 362 sheet: 0.24 (0.80), residues: 49 loop : -2.34 (0.53), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 86 HIS 0.003 0.001 HIS A 248 PHE 0.007 0.001 PHE A 236 TYR 0.010 0.001 TYR A 335 ARG 0.003 0.000 ARG A 111 *********************** 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 73 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 49 time to evaluate : 0.414 Fit side-chains REVERT: A 69 ASN cc_start: 0.7972 (OUTLIER) cc_final: 0.7598 (m110) REVERT: A 285 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7763 (mp) REVERT: A 430 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8113 (mm) outliers start: 24 outliers final: 16 residues processed: 68 average time/residue: 0.1836 time to fit residues: 15.7490 Evaluate side-chains 68 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 49 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 112 HIS Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 497 ARG Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 6 GLU Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 79 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 5 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 38 optimal weight: 0.3980 chunk 44 optimal weight: 6.9990 chunk 29 optimal weight: 0.3980 chunk 53 optimal weight: 0.0970 chunk 33 optimal weight: 0.0980 chunk 32 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 overall best weight: 0.3378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 4410 Z= 0.162 Angle : 0.504 8.586 5996 Z= 0.246 Chirality : 0.037 0.134 711 Planarity : 0.004 0.058 733 Dihedral : 6.960 56.629 636 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.48 % Allowed : 25.22 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.38), residues: 552 helix: 2.56 (0.27), residues: 362 sheet: 0.75 (0.81), residues: 47 loop : -2.27 (0.53), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 161 HIS 0.002 0.001 HIS A 248 PHE 0.006 0.001 PHE A 236 TYR 0.009 0.001 TYR A 335 ARG 0.004 0.000 ARG A 111 *********************** 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 66 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 50 time to evaluate : 0.477 Fit side-chains REVERT: A 69 ASN cc_start: 0.7878 (OUTLIER) cc_final: 0.7530 (m110) REVERT: A 430 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.8112 (mm) outliers start: 16 outliers final: 9 residues processed: 63 average time/residue: 0.1955 time to fit residues: 15.4330 Evaluate side-chains 61 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 50 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 112 HIS Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 497 ARG Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 74 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 15 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 0.0970 chunk 36 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.1818 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= 0.197 Angle : 0.503 8.355 5996 Z= 0.250 Chirality : 0.037 0.135 711 Planarity : 0.004 0.057 733 Dihedral : 6.700 59.558 633 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.48 % Allowed : 25.00 % Favored : 71.52 % 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: 1.88 (0.38), residues: 552 helix: 2.54 (0.27), residues: 362 sheet: 0.87 (0.82), residues: 47 loop : -2.27 (0.53), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 161 HIS 0.003 0.001 HIS A 248 PHE 0.006 0.001 PHE B 29 TYR 0.010 0.001 TYR A 335 ARG 0.004 0.000 ARG A 111 *********************** 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 65 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 49 time to evaluate : 0.486 Fit side-chains REVERT: A 69 ASN cc_start: 0.7905 (OUTLIER) cc_final: 0.7566 (m110) REVERT: A 285 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7742 (mp) REVERT: A 430 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8129 (mm) outliers start: 16 outliers final: 10 residues processed: 63 average time/residue: 0.2064 time to fit residues: 16.1274 Evaluate side-chains 62 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 49 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 112 HIS Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 497 ARG Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 74 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 50 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 15 optimal weight: 0.2980 chunk 44 optimal weight: 6.9990 chunk 46 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 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 69 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.1855 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= 0.206 Angle : 0.505 8.135 5996 Z= 0.251 Chirality : 0.037 0.134 711 Planarity : 0.004 0.057 733 Dihedral : 6.656 58.647 633 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 3.26 % Allowed : 24.78 % Favored : 71.96 % 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: 1.84 (0.38), residues: 552 helix: 2.51 (0.27), residues: 362 sheet: 0.89 (0.83), residues: 47 loop : -2.29 (0.52), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 161 HIS 0.003 0.001 HIS A 248 PHE 0.006 0.001 PHE B 29 TYR 0.010 0.001 TYR A 335 ARG 0.004 0.000 ARG A 111 *********************** 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 62 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 47 time to evaluate : 0.482 Fit side-chains REVERT: A 69 ASN cc_start: 0.7849 (OUTLIER) cc_final: 0.7509 (m110) REVERT: A 251 LEU cc_start: 0.6977 (OUTLIER) cc_final: 0.6768 (tt) REVERT: A 285 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7738 (mp) REVERT: A 430 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8138 (mm) outliers start: 15 outliers final: 10 residues processed: 60 average time/residue: 0.2073 time to fit residues: 15.6660 Evaluate side-chains 61 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 47 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 112 HIS Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 497 ARG Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 74 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 24 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 26 optimal weight: 0.3980 chunk 34 optimal weight: 0.0470 chunk 46 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.6082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4410 Z= 0.209 Angle : 0.519 8.050 5996 Z= 0.258 Chirality : 0.038 0.135 711 Planarity : 0.004 0.057 733 Dihedral : 6.405 54.539 633 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.26 % Allowed : 25.00 % Favored : 71.74 % 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: 1.82 (0.38), residues: 552 helix: 2.48 (0.27), residues: 362 sheet: 0.99 (0.83), residues: 47 loop : -2.28 (0.52), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 161 HIS 0.003 0.001 HIS A 248 PHE 0.009 0.001 PHE A 64 TYR 0.010 0.001 TYR A 335 ARG 0.004 0.000 ARG A 111 ********************** 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 62 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 47 time to evaluate : 0.482 Fit side-chains REVERT: A 69 ASN cc_start: 0.7819 (OUTLIER) cc_final: 0.7558 (m110) REVERT: A 251 LEU cc_start: 0.7034 (OUTLIER) cc_final: 0.6803 (tt) REVERT: A 285 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7741 (mp) REVERT: A 430 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8141 (mm) outliers start: 15 outliers final: 10 residues processed: 60 average time/residue: 0.1932 time to fit residues: 14.6498 Evaluate side-chains 60 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 46 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 112 HIS Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 497 ARG Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 74 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 40 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 44 optimal weight: 9.9990 chunk 5 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 31 optimal weight: 0.0980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.178890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.144870 restraints weight = 4335.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.144870 restraints weight = 4217.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.144870 restraints weight = 4217.324| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4410 Z= 0.197 Angle : 0.504 8.008 5996 Z= 0.249 Chirality : 0.037 0.135 711 Planarity : 0.004 0.057 733 Dihedral : 6.109 51.260 633 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.61 % Allowed : 25.87 % Favored : 71.52 % 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: 1.86 (0.38), residues: 552 helix: 2.50 (0.27), residues: 362 sheet: 1.16 (0.83), residues: 47 loop : -2.29 (0.52), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 161 HIS 0.003 0.001 HIS A 248 PHE 0.007 0.001 PHE A 64 TYR 0.010 0.001 TYR A 335 ARG 0.004 0.000 ARG A 111 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1158.37 seconds wall clock time: 21 minutes 38.75 seconds (1298.75 seconds total)