Starting phenix.real_space_refine on Sun Aug 4 02:50:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bis_44600/08_2024/9bis_44600_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bis_44600/08_2024/9bis_44600.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bis_44600/08_2024/9bis_44600.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bis_44600/08_2024/9bis_44600.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bis_44600/08_2024/9bis_44600_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bis_44600/08_2024/9bis_44600_trim.cif" } resolution = 3.2 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= 0.028 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 S 34 5.16 5 C 3098 2.51 5 N 767 2.21 5 O 811 1.98 5 H 4734 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 178": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 9444 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 7529 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 21, 'TRANS': 450} Chain breaks: 1 Chain: "B" Number of atoms: 1890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1890 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'AXL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.65, per 1000 atoms: 0.60 Number of scatterers: 9444 At special positions: 0 Unit cell: (94.928, 108.19, 76.78, 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 34 16.00 O 811 8.00 N 767 7.00 C 3098 6.00 H 4734 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 211 " - pdb=" SG CYS A 216 " 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: 7.41 Conformation dependent library (CDL) restraints added in 888.9 milliseconds 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1104 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 2 sheets defined 63.0% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 43 through 45 No H-bonds generated for 'chain 'A' and resid 43 through 45' Processing helix chain 'A' and resid 46 through 74 removed outlier: 3.637A pdb=" N VAL A 51 " --> pdb=" O ALA A 47 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ASN A 52 " --> pdb=" O PHE A 48 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N VAL A 66 " --> pdb=" O GLY A 62 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N THR A 68 " --> pdb=" O LYS A 64 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N LEU A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 96 Processing helix chain 'A' and resid 96 through 107 removed outlier: 3.574A pdb=" N TRP A 107 " --> pdb=" O ILE A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 132 removed outlier: 3.541A pdb=" N VAL A 120 " --> pdb=" O TYR A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 171 removed outlier: 4.258A pdb=" N GLY A 159 " --> pdb=" O LEU A 155 " (cutoff:3.500A) Proline residue: A 162 - end of helix removed outlier: 3.843A pdb=" N ALA A 165 " --> pdb=" O LYS A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 206 removed outlier: 3.662A pdb=" N ARG A 180 " --> pdb=" O HIS A 176 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR A 181 " --> pdb=" O ALA A 177 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG A 182 " --> pdb=" O GLU A 178 " (cutoff:3.500A) Proline residue: A 203 - end of helix removed outlier: 3.674A pdb=" N ARG A 206 " --> pdb=" O THR A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 238 removed outlier: 3.869A pdb=" N ALA A 220 " --> pdb=" O CYS A 216 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE A 221 " --> pdb=" O TYR A 217 " (cutoff:3.500A) Proline residue: A 224 - end of helix removed outlier: 3.855A pdb=" N GLY A 238 " --> pdb=" O VAL A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 242 Processing helix chain 'A' and resid 250 through 266 removed outlier: 3.974A pdb=" N ARG A 266 " --> pdb=" O ALA A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 307 removed outlier: 3.535A pdb=" N ASP A 295 " --> pdb=" O HIS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 318 removed outlier: 3.729A pdb=" N PHE A 312 " --> pdb=" O PRO A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 329 removed outlier: 3.783A pdb=" N LYS A 329 " --> pdb=" O LEU A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 345 Processing helix chain 'A' and resid 346 through 362 Proline residue: A 357 - end of helix Processing helix chain 'A' and resid 362 through 370 removed outlier: 4.054A pdb=" N CYS A 370 " --> pdb=" O LEU A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 403 Processing helix chain 'A' and resid 611 through 636 removed outlier: 3.517A pdb=" N THR A 628 " --> pdb=" O MET A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 640 No H-bonds generated for 'chain 'A' and resid 638 through 640' Processing helix chain 'A' and resid 641 through 665 removed outlier: 3.982A pdb=" N LEU A 645 " --> pdb=" O MET A 641 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLN A 646 " --> pdb=" O LYS A 642 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA A 647 " --> pdb=" O SER A 643 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLN A 665 " --> pdb=" O LEU A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 695 removed outlier: 3.866A pdb=" N TYR A 695 " --> pdb=" O VAL A 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 30 No H-bonds generated for 'chain 'B' and resid 28 through 30' Processing helix chain 'B' and resid 53 through 56 removed outlier: 4.200A pdb=" N ARG B 56 " --> pdb=" O TRP B 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 53 through 56' Processing sheet with id=AA1, first strand: chain 'B' and resid 18 through 23 Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 60 removed outlier: 6.416A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N SER B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N MET B 34 " --> pdb=" O SER B 50 " (cutoff:3.500A) 275 hydrogen bonds defined for protein. 804 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: 3.11 Time building geometry restraints manager: 7.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 4724 1.04 - 1.24: 645 1.24 - 1.45: 1475 1.45 - 1.65: 2672 1.65 - 1.85: 54 Bond restraints: 9570 Sorted by residual: bond pdb=" C GLU B 111 " pdb=" O GLU B 111 " ideal model delta sigma weight residual 1.236 1.198 0.038 1.26e-02 6.30e+03 9.09e+00 bond pdb=" N MET B 79 " pdb=" CA MET B 79 " ideal model delta sigma weight residual 1.455 1.490 -0.035 1.23e-02 6.61e+03 8.05e+00 bond pdb=" N GLU B 111 " pdb=" H GLU B 111 " ideal model delta sigma weight residual 0.860 0.915 -0.055 2.00e-02 2.50e+03 7.48e+00 bond pdb=" C MET B 79 " pdb=" O MET B 79 " ideal model delta sigma weight residual 1.235 1.200 0.035 1.28e-02 6.10e+03 7.36e+00 bond pdb=" C3 AXL A 801 " pdb=" S4 AXL A 801 " ideal model delta sigma weight residual 1.867 1.814 0.053 2.00e-02 2.50e+03 6.99e+00 ... (remaining 9565 not shown) Histogram of bond angle deviations from ideal: 84.77 - 95.02: 2 95.02 - 105.28: 85 105.28 - 115.53: 11929 115.53 - 125.78: 5137 125.78 - 136.04: 128 Bond angle restraints: 17281 Sorted by residual: angle pdb=" C2 AXL A 801 " pdb=" C3 AXL A 801 " pdb=" N7 AXL A 801 " ideal model delta sigma weight residual 112.29 87.78 24.51 3.00e+00 1.11e-01 6.68e+01 angle pdb=" C1 AXL A 801 " pdb=" C2 AXL A 801 " pdb=" C3 AXL A 801 " ideal model delta sigma weight residual 107.79 84.77 23.02 3.00e+00 1.11e-01 5.89e+01 angle pdb=" CA ASN B 109 " pdb=" CB ASN B 109 " pdb=" CG ASN B 109 " ideal model delta sigma weight residual 112.60 116.94 -4.34 1.00e+00 1.00e+00 1.88e+01 angle pdb=" CA PHE B 113 " pdb=" C PHE B 113 " pdb=" O PHE B 113 " ideal model delta sigma weight residual 120.82 116.57 4.25 1.05e+00 9.07e-01 1.64e+01 angle pdb=" CA PHE B 113 " pdb=" CB PHE B 113 " pdb=" CG PHE B 113 " ideal model delta sigma weight residual 113.80 117.79 -3.99 1.00e+00 1.00e+00 1.59e+01 ... (remaining 17276 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.63: 4211 25.63 - 51.26: 270 51.26 - 76.89: 51 76.89 - 102.52: 7 102.52 - 128.15: 6 Dihedral angle restraints: 4545 sinusoidal: 2406 harmonic: 2139 Sorted by residual: dihedral pdb=" CA TRP A 283 " pdb=" C TRP A 283 " pdb=" N ALA A 284 " pdb=" CA ALA A 284 " ideal model delta harmonic sigma weight residual 180.00 154.78 25.22 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" SG CYS A 211 " pdb=" CB CYS A 216 " pdb=" SG CYS A 216 " pdb=" CA CYS A 216 " ideal model delta sinusoidal sigma weight residual -73.00 0.98 -73.98 1 2.00e+01 2.50e-03 1.74e+01 dihedral pdb=" C52 AXL A 801 " pdb=" C5 AXL A 801 " pdb=" C6 AXL A 801 " pdb=" C61 AXL A 801 " ideal model delta sinusoidal sigma weight residual -25.58 -153.73 128.15 1 3.00e+01 1.11e-03 1.73e+01 ... (remaining 4542 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 724 0.104 - 0.207: 13 0.207 - 0.311: 0 0.311 - 0.414: 1 0.414 - 0.518: 1 Chirality restraints: 739 Sorted by residual: chirality pdb=" C3 AXL A 801 " pdb=" C2 AXL A 801 " pdb=" N7 AXL A 801 " pdb=" S4 AXL A 801 " both_signs ideal model delta sigma weight residual False 2.97 3.49 -0.52 2.00e-01 2.50e+01 6.70e+00 chirality pdb=" C2 AXL A 801 " pdb=" C1 AXL A 801 " pdb=" C3 AXL A 801 " pdb=" N8 AXL A 801 " both_signs ideal model delta sigma weight residual False 2.36 2.75 -0.39 2.00e-01 2.50e+01 3.78e+00 chirality pdb=" CA MET B 79 " pdb=" N MET B 79 " pdb=" C MET B 79 " pdb=" CB MET B 79 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.42e-01 ... (remaining 736 not shown) Planarity restraints: 1379 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 109 " 0.147 2.00e-02 2.50e+03 4.29e-01 2.76e+03 pdb=" CG ASN B 109 " -0.021 2.00e-02 2.50e+03 pdb=" OD1 ASN B 109 " -0.139 2.00e-02 2.50e+03 pdb=" ND2 ASN B 109 " -0.001 2.00e-02 2.50e+03 pdb="HD21 ASN B 109 " -0.722 2.00e-02 2.50e+03 pdb="HD22 ASN B 109 " 0.737 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 AXL A 801 " -0.041 2.00e-02 2.50e+03 2.10e-02 8.86e+00 pdb=" C12 AXL A 801 " 0.022 2.00e-02 2.50e+03 pdb=" C13 AXL A 801 " 0.018 2.00e-02 2.50e+03 pdb=" C14 AXL A 801 " 0.005 2.00e-02 2.50e+03 pdb=" C15 AXL A 801 " -0.001 2.00e-02 2.50e+03 pdb=" C16 AXL A 801 " 0.005 2.00e-02 2.50e+03 pdb=" C17 AXL A 801 " 0.018 2.00e-02 2.50e+03 pdb=" O18 AXL A 801 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 87 " 0.038 5.00e-02 4.00e+02 5.67e-02 5.15e+00 pdb=" N PRO B 88 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO B 88 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 88 " 0.032 5.00e-02 4.00e+02 ... (remaining 1376 not shown) Histogram of nonbonded interaction distances: 1.38 - 2.02: 85 2.02 - 2.67: 13722 2.67 - 3.31: 27674 3.31 - 3.96: 35209 3.96 - 4.60: 55261 Nonbonded interactions: 131951 Sorted by model distance: nonbonded pdb=" C1 AXL A 801 " pdb=" N7 AXL A 801 " model vdw 1.376 2.600 nonbonded pdb=" O TRP B 53 " pdb=" HG SER B 54 " model vdw 1.654 2.450 nonbonded pdb=" OD1 ASP A 333 " pdb=" H LEU A 334 " model vdw 1.682 2.450 nonbonded pdb=" HZ3 LYS A 329 " pdb=" OE2 GLU A 398 " model vdw 1.687 2.450 nonbonded pdb=" O ILE A 114 " pdb=" HG SER A 118 " model vdw 1.706 2.450 ... (remaining 131946 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.740 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: 0.140 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 33.590 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.040 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 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 : 0.004 0.053 4836 Z= 0.249 Angle : 0.777 24.513 6571 Z= 0.391 Chirality : 0.045 0.518 739 Planarity : 0.004 0.057 812 Dihedral : 18.673 128.146 1729 Min Nonbonded Distance : 1.376 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 0.40 % Allowed : 20.80 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.35), residues: 589 helix: 1.56 (0.29), residues: 325 sheet: -1.84 (0.66), residues: 58 loop : -1.89 (0.42), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 36 HIS 0.001 0.000 HIS A 279 PHE 0.031 0.001 PHE B 113 TYR 0.023 0.001 TYR A 94 ARG 0.003 0.000 ARG B 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 63 time to evaluate : 0.720 Fit side-chains REVERT: B 111 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7322 (mt-10) outliers start: 2 outliers final: 1 residues processed: 65 average time/residue: 0.3612 time to fit residues: 30.5677 Evaluate side-chains 62 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 60 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain B residue 111 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 49 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 24 optimal weight: 0.0670 chunk 15 optimal weight: 0.9980 chunk 30 optimal weight: 0.0470 chunk 23 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 overall best weight: 0.5616 ------------------------------------------------------------------------------- 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: 0.8002 moved from start: 0.0559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4836 Z= 0.213 Angle : 0.561 5.669 6571 Z= 0.296 Chirality : 0.038 0.155 739 Planarity : 0.004 0.056 812 Dihedral : 14.413 128.757 685 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 1.20 % Allowed : 20.80 % Favored : 78.00 % 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: 0.37 (0.35), residues: 589 helix: 1.68 (0.28), residues: 336 sheet: -1.66 (0.68), residues: 57 loop : -1.74 (0.42), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 107 HIS 0.003 0.001 HIS A 291 PHE 0.010 0.001 PHE A 58 TYR 0.016 0.001 TYR A 94 ARG 0.002 0.000 ARG B 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 64 time to evaluate : 0.663 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 69 average time/residue: 0.3397 time to fit residues: 30.5081 Evaluate side-chains 61 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 59 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 276 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 29 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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: 0.8037 moved from start: 0.0861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4836 Z= 0.293 Angle : 0.562 5.762 6571 Z= 0.301 Chirality : 0.038 0.153 739 Planarity : 0.004 0.058 812 Dihedral : 13.875 131.928 682 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 1.60 % Allowed : 21.40 % Favored : 77.00 % 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: 0.42 (0.35), residues: 589 helix: 1.70 (0.28), residues: 336 sheet: -1.42 (0.69), residues: 57 loop : -1.76 (0.42), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 107 HIS 0.002 0.000 HIS A 291 PHE 0.014 0.001 PHE B 113 TYR 0.014 0.001 TYR A 94 ARG 0.002 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 60 time to evaluate : 0.783 Fit side-chains revert: symmetry clash REVERT: A 404 MET cc_start: 0.6054 (OUTLIER) cc_final: 0.4530 (pmm) REVERT: B 85 ASN cc_start: 0.7735 (t0) cc_final: 0.7498 (t0) outliers start: 8 outliers final: 6 residues processed: 66 average time/residue: 0.4202 time to fit residues: 35.6098 Evaluate side-chains 63 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 56 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 266 ARG Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 58 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 27 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 25 optimal weight: 0.4980 chunk 36 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.8023 moved from start: 0.0987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4836 Z= 0.236 Angle : 0.540 5.720 6571 Z= 0.289 Chirality : 0.038 0.159 739 Planarity : 0.004 0.055 812 Dihedral : 13.721 126.521 682 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 2.00 % Allowed : 21.00 % Favored : 77.00 % 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: 0.52 (0.35), residues: 589 helix: 1.81 (0.28), residues: 336 sheet: -1.32 (0.68), residues: 59 loop : -1.79 (0.43), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 107 HIS 0.002 0.000 HIS A 291 PHE 0.012 0.001 PHE A 58 TYR 0.009 0.001 TYR A 183 ARG 0.002 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 61 time to evaluate : 0.657 Fit side-chains revert: symmetry clash REVERT: A 404 MET cc_start: 0.6054 (OUTLIER) cc_final: 0.4550 (pmm) REVERT: B 85 ASN cc_start: 0.7716 (t0) cc_final: 0.7496 (t0) outliers start: 10 outliers final: 7 residues processed: 68 average time/residue: 0.3847 time to fit residues: 33.1755 Evaluate side-chains 67 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 59 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 266 ARG Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 58 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 0 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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: 0.8044 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4836 Z= 0.287 Angle : 0.552 5.757 6571 Z= 0.296 Chirality : 0.038 0.158 739 Planarity : 0.004 0.057 812 Dihedral : 13.658 128.174 682 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 2.60 % Allowed : 20.20 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.35), residues: 589 helix: 1.79 (0.28), residues: 336 sheet: -1.30 (0.68), residues: 59 loop : -1.78 (0.43), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 107 HIS 0.002 0.000 HIS A 291 PHE 0.016 0.002 PHE A 350 TYR 0.010 0.001 TYR A 634 ARG 0.002 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 56 time to evaluate : 0.729 Fit side-chains revert: symmetry clash REVERT: A 404 MET cc_start: 0.6163 (OUTLIER) cc_final: 0.4670 (pmm) REVERT: B 85 ASN cc_start: 0.7731 (t0) cc_final: 0.7500 (t0) outliers start: 13 outliers final: 10 residues processed: 66 average time/residue: 0.4090 time to fit residues: 33.9598 Evaluate side-chains 67 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 56 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 266 ARG Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 106 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 14 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 55 optimal weight: 0.0050 chunk 6 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- 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: 0.8020 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4836 Z= 0.208 Angle : 0.526 5.690 6571 Z= 0.281 Chirality : 0.037 0.158 739 Planarity : 0.004 0.055 812 Dihedral : 13.537 124.614 682 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 2.60 % Allowed : 19.40 % Favored : 78.00 % 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: 0.62 (0.36), residues: 589 helix: 1.92 (0.28), residues: 336 sheet: -1.28 (0.67), residues: 59 loop : -1.80 (0.44), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 649 HIS 0.002 0.000 HIS A 291 PHE 0.011 0.001 PHE A 58 TYR 0.010 0.001 TYR A 183 ARG 0.002 0.000 ARG B 72 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 59 time to evaluate : 0.714 Fit side-chains revert: symmetry clash REVERT: A 404 MET cc_start: 0.6137 (OUTLIER) cc_final: 0.4704 (pmm) REVERT: B 85 ASN cc_start: 0.7721 (t0) cc_final: 0.7505 (t0) outliers start: 13 outliers final: 9 residues processed: 69 average time/residue: 0.3692 time to fit residues: 32.6389 Evaluate side-chains 65 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 55 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 266 ARG Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 58 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 32 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 31 optimal weight: 0.3980 chunk 56 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 33 optimal weight: 0.3980 chunk 17 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.8025 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4836 Z= 0.227 Angle : 0.527 5.685 6571 Z= 0.282 Chirality : 0.037 0.158 739 Planarity : 0.004 0.055 812 Dihedral : 13.478 125.238 682 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 2.80 % Allowed : 19.20 % Favored : 78.00 % 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: 0.65 (0.36), residues: 589 helix: 1.94 (0.28), residues: 336 sheet: -1.36 (0.66), residues: 59 loop : -1.75 (0.44), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 107 HIS 0.003 0.000 HIS A 291 PHE 0.020 0.001 PHE B 80 TYR 0.010 0.001 TYR A 183 ARG 0.002 0.000 ARG B 72 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 56 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 337 PHE cc_start: 0.7200 (t80) cc_final: 0.6992 (t80) REVERT: A 404 MET cc_start: 0.6109 (OUTLIER) cc_final: 0.4655 (pmm) REVERT: B 85 ASN cc_start: 0.7724 (t0) cc_final: 0.7505 (t0) outliers start: 14 outliers final: 10 residues processed: 67 average time/residue: 0.4021 time to fit residues: 33.8760 Evaluate side-chains 67 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 56 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 266 ARG Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 106 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 11 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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: 0.8039 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4836 Z= 0.273 Angle : 0.545 5.717 6571 Z= 0.291 Chirality : 0.038 0.158 739 Planarity : 0.004 0.056 812 Dihedral : 13.467 125.491 682 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 2.60 % Allowed : 19.40 % Favored : 78.00 % 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: 0.56 (0.35), residues: 589 helix: 1.86 (0.28), residues: 336 sheet: -1.37 (0.67), residues: 59 loop : -1.80 (0.44), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 107 HIS 0.001 0.000 HIS A 279 PHE 0.016 0.002 PHE B 80 TYR 0.011 0.001 TYR A 634 ARG 0.002 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 58 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 404 MET cc_start: 0.6122 (OUTLIER) cc_final: 0.4766 (pmm) REVERT: B 85 ASN cc_start: 0.7697 (t0) cc_final: 0.7486 (t0) outliers start: 13 outliers final: 10 residues processed: 68 average time/residue: 0.3796 time to fit residues: 32.7536 Evaluate side-chains 67 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 56 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 266 ARG Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 106 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 23 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 38 optimal weight: 0.4980 chunk 58 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.8033 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4836 Z= 0.235 Angle : 0.536 5.693 6571 Z= 0.287 Chirality : 0.037 0.157 739 Planarity : 0.004 0.055 812 Dihedral : 13.373 123.912 682 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 2.20 % Allowed : 19.60 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.36), residues: 589 helix: 1.92 (0.28), residues: 336 sheet: -1.39 (0.66), residues: 59 loop : -1.80 (0.44), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 107 HIS 0.002 0.000 HIS A 291 PHE 0.016 0.001 PHE B 80 TYR 0.010 0.001 TYR A 183 ARG 0.002 0.000 ARG B 67 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 58 time to evaluate : 0.723 Fit side-chains revert: symmetry clash REVERT: A 404 MET cc_start: 0.6066 (OUTLIER) cc_final: 0.4690 (pmm) REVERT: B 85 ASN cc_start: 0.7745 (t0) cc_final: 0.7523 (t0) outliers start: 11 outliers final: 9 residues processed: 66 average time/residue: 0.3891 time to fit residues: 32.6903 Evaluate side-chains 67 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 57 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 106 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 1.9990 chunk 46 optimal weight: 0.0980 chunk 4 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.8032 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4836 Z= 0.228 Angle : 0.539 5.678 6571 Z= 0.287 Chirality : 0.037 0.157 739 Planarity : 0.004 0.055 812 Dihedral : 13.267 123.846 682 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 1.80 % Allowed : 20.00 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.36), residues: 589 helix: 1.93 (0.28), residues: 336 sheet: -1.39 (0.66), residues: 59 loop : -1.81 (0.43), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 117 HIS 0.002 0.000 HIS A 279 PHE 0.016 0.001 PHE B 80 TYR 0.010 0.001 TYR A 183 ARG 0.003 0.000 ARG B 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 58 time to evaluate : 0.706 Fit side-chains revert: symmetry clash REVERT: A 404 MET cc_start: 0.6005 (OUTLIER) cc_final: 0.4635 (pmm) REVERT: B 53 TRP cc_start: 0.7984 (p-90) cc_final: 0.7689 (p-90) REVERT: B 85 ASN cc_start: 0.7716 (t0) cc_final: 0.7512 (t0) outliers start: 9 outliers final: 8 residues processed: 64 average time/residue: 0.3818 time to fit residues: 30.9692 Evaluate side-chains 66 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 57 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 106 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 46 optimal weight: 0.9990 chunk 19 optimal weight: 0.4980 chunk 48 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 33 optimal weight: 0.0170 chunk 53 optimal weight: 1.9990 chunk 31 optimal weight: 0.0050 chunk 40 optimal weight: 0.5980 overall best weight: 0.3832 ------------------------------------------------------------------------------- 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 = 0.3705 r_free = 0.3705 target = 0.134883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.110046 restraints weight = 19289.199| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.55 r_work: 0.3261 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4836 Z= 0.179 Angle : 0.522 5.614 6571 Z= 0.278 Chirality : 0.037 0.157 739 Planarity : 0.004 0.055 812 Dihedral : 13.021 122.906 678 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 1.60 % Allowed : 20.60 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.36), residues: 589 helix: 2.07 (0.28), residues: 337 sheet: -1.39 (0.66), residues: 59 loop : -1.76 (0.43), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 649 HIS 0.002 0.000 HIS A 279 PHE 0.015 0.001 PHE B 80 TYR 0.010 0.001 TYR A 183 ARG 0.002 0.000 ARG B 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3028.17 seconds wall clock time: 53 minutes 52.57 seconds (3232.57 seconds total)