Starting phenix.real_space_refine on Sat May 2 11:58:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l1a_62739/05_2026/9l1a_62739_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l1a_62739/05_2026/9l1a_62739.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9l1a_62739/05_2026/9l1a_62739.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l1a_62739/05_2026/9l1a_62739.map" model { file = "/net/cci-nas-00/data/ceres_data/9l1a_62739/05_2026/9l1a_62739_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l1a_62739/05_2026/9l1a_62739_trim.cif" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= -0.003 sd= 0.107 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: 6 Type Number sf(0) Gaussians S 32 5.16 5 Cl 1 4.86 5 Na 1 4.78 5 C 2981 2.51 5 N 662 2.21 5 O 745 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4422 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4319 Classifications: {'peptide': 542} Link IDs: {'PTRANS': 28, 'TRANS': 513} Chain breaks: 1 Chain: "A" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 103 Unusual residues: {' CL': 1, ' NA': 1, 'CLR': 1, 'Y01': 2} Classifications: {'undetermined': 5, 'water': 3} Link IDs: {None: 7} Time building chain proxies: 0.84, per 1000 atoms: 0.19 Number of scatterers: 4422 At special positions: 0 Unit cell: (76.824, 67.221, 92.829, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 32 16.00 Na 1 11.00 O 745 8.00 N 662 7.00 C 2981 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 171 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 0.21 Conformation dependent library (CDL) restraints added in 88.3 milliseconds 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 986 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 1 sheets defined 79.7% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'A' and resid 50 through 59 removed outlier: 4.041A pdb=" N GLY A 57 " --> pdb=" O SER A 53 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N PHE A 58 " --> pdb=" O VAL A 54 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL A 59 " --> pdb=" O ALA A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 65 Processing helix chain 'A' and resid 65 through 74 removed outlier: 3.636A pdb=" N TYR A 69 " --> pdb=" O TRP A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 90 Processing helix chain 'A' and resid 90 through 106 Processing helix chain 'A' and resid 110 through 117 removed outlier: 3.731A pdb=" N GLU A 114 " --> pdb=" O ILE A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 151 removed outlier: 3.893A pdb=" N TYR A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR A 137 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE A 139 " --> pdb=" O ASN A 135 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N VAL A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE A 141 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU A 142 " --> pdb=" O TYR A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 177 removed outlier: 3.504A pdb=" N ARG A 177 " --> pdb=" O ASP A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 202 Processing helix chain 'A' and resid 217 through 238 Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 250 through 267 removed outlier: 4.488A pdb=" N PHE A 254 " --> pdb=" O ALA A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 279 removed outlier: 3.629A pdb=" N GLY A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 286 removed outlier: 3.688A pdb=" N GLU A 286 " --> pdb=" O THR A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 302 removed outlier: 4.295A pdb=" N TRP A 291 " --> pdb=" O ASP A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 315 removed outlier: 3.766A pdb=" N TYR A 315 " --> pdb=" O SER A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 356 removed outlier: 4.398A pdb=" N ASP A 325 " --> pdb=" O ASN A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 362 Processing helix chain 'A' and resid 369 through 379 removed outlier: 3.704A pdb=" N TYR A 374 " --> pdb=" O ALA A 370 " (cutoff:3.500A) Proline residue: A 375 - end of helix removed outlier: 3.550A pdb=" N THR A 379 " --> pdb=" O PRO A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 418 removed outlier: 3.673A pdb=" N TRP A 387 " --> pdb=" O LEU A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 423 Processing helix chain 'A' and resid 425 through 444 removed outlier: 3.979A pdb=" N GLU A 429 " --> pdb=" O GLY A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 461 removed outlier: 3.817A pdb=" N VAL A 454 " --> pdb=" O GLY A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 482 Processing helix chain 'A' and resid 484 through 497 Processing helix chain 'A' and resid 501 through 510 removed outlier: 4.410A pdb=" N LYS A 505 " --> pdb=" O GLY A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 526 Processing helix chain 'A' and resid 539 through 555 removed outlier: 4.185A pdb=" N SER A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 568 Processing helix chain 'A' and resid 571 through 581 Processing helix chain 'A' and resid 586 through 593 Processing sheet with id=AA1, first strand: chain 'A' and resid 531 through 532 284 hydrogen bonds defined for protein. 834 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: 0.35 Time building geometry restraints manager: 0.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 652 1.32 - 1.44: 1367 1.44 - 1.56: 2503 1.56 - 1.69: 0 1.69 - 1.81: 46 Bond restraints: 4568 Sorted by residual: bond pdb=" N VAL A 59 " pdb=" CA VAL A 59 " ideal model delta sigma weight residual 1.459 1.505 -0.046 1.25e-02 6.40e+03 1.33e+01 bond pdb=" N ARG A 177 " pdb=" CA ARG A 177 " ideal model delta sigma weight residual 1.458 1.500 -0.042 1.30e-02 5.92e+03 1.05e+01 bond pdb=" N VAL A 239 " pdb=" CA VAL A 239 " ideal model delta sigma weight residual 1.461 1.498 -0.038 1.19e-02 7.06e+03 1.00e+01 bond pdb=" N ILE A 210 " pdb=" CA ILE A 210 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.30e-02 5.92e+03 9.44e+00 bond pdb=" N TRP A 166 " pdb=" CA TRP A 166 " ideal model delta sigma weight residual 1.456 1.493 -0.038 1.26e-02 6.30e+03 8.87e+00 ... (remaining 4563 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 5734 1.20 - 2.41: 330 2.41 - 3.61: 133 3.61 - 4.82: 41 4.82 - 6.02: 9 Bond angle restraints: 6247 Sorted by residual: angle pdb=" N CYS A 305 " pdb=" CA CYS A 305 " pdb=" C CYS A 305 " ideal model delta sigma weight residual 113.23 107.63 5.60 1.22e+00 6.72e-01 2.11e+01 angle pdb=" C HIS A 212 " pdb=" N PRO A 213 " pdb=" CA PRO A 213 " ideal model delta sigma weight residual 119.05 123.44 -4.39 1.11e+00 8.12e-01 1.57e+01 angle pdb=" CA ASN A 167 " pdb=" C ASN A 167 " pdb=" O ASN A 167 " ideal model delta sigma weight residual 120.38 116.21 4.17 1.09e+00 8.42e-01 1.47e+01 angle pdb=" CA VAL A 239 " pdb=" C VAL A 239 " pdb=" O VAL A 239 " ideal model delta sigma weight residual 120.95 117.04 3.91 1.04e+00 9.25e-01 1.41e+01 angle pdb=" C MET A 176 " pdb=" N ARG A 177 " pdb=" CA ARG A 177 " ideal model delta sigma weight residual 120.60 126.57 -5.97 1.60e+00 3.91e-01 1.39e+01 ... (remaining 6242 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.31: 2368 16.31 - 32.62: 255 32.62 - 48.93: 78 48.93 - 65.24: 22 65.24 - 81.55: 4 Dihedral angle restraints: 2727 sinusoidal: 1167 harmonic: 1560 Sorted by residual: dihedral pdb=" CB CYS A 162 " pdb=" SG CYS A 162 " pdb=" SG CYS A 171 " pdb=" CB CYS A 171 " ideal model delta sinusoidal sigma weight residual -86.00 -117.91 31.91 1 1.00e+01 1.00e-02 1.45e+01 dihedral pdb=" CA GLU A 114 " pdb=" CB GLU A 114 " pdb=" CG GLU A 114 " pdb=" CD GLU A 114 " ideal model delta sinusoidal sigma weight residual -180.00 -121.38 -58.62 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CB MET A 327 " pdb=" CG MET A 327 " pdb=" SD MET A 327 " pdb=" CE MET A 327 " ideal model delta sinusoidal sigma weight residual 180.00 124.54 55.46 3 1.50e+01 4.44e-03 9.35e+00 ... (remaining 2724 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 507 0.043 - 0.086: 131 0.086 - 0.129: 39 0.129 - 0.172: 7 0.172 - 0.214: 7 Chirality restraints: 691 Sorted by residual: chirality pdb=" CA ILE A 210 " pdb=" N ILE A 210 " pdb=" C ILE A 210 " pdb=" CB ILE A 210 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA HIS A 212 " pdb=" N HIS A 212 " pdb=" C HIS A 212 " pdb=" CB HIS A 212 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA LYS A 178 " pdb=" N LYS A 178 " pdb=" C LYS A 178 " pdb=" CB LYS A 178 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 688 not shown) Planarity restraints: 749 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 165 " 0.011 2.00e-02 2.50e+03 2.21e-02 4.89e+00 pdb=" C SER A 165 " -0.038 2.00e-02 2.50e+03 pdb=" O SER A 165 " 0.014 2.00e-02 2.50e+03 pdb=" N TRP A 166 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 581 " 0.031 5.00e-02 4.00e+02 4.78e-02 3.66e+00 pdb=" N PRO A 582 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 582 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 582 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 58 " 0.009 2.00e-02 2.50e+03 1.84e-02 3.40e+00 pdb=" C PHE A 58 " -0.032 2.00e-02 2.50e+03 pdb=" O PHE A 58 " 0.012 2.00e-02 2.50e+03 pdb=" N VAL A 59 " 0.011 2.00e-02 2.50e+03 ... (remaining 746 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 702 2.75 - 3.29: 4458 3.29 - 3.83: 7627 3.83 - 4.36: 9479 4.36 - 4.90: 16174 Nonbonded interactions: 38440 Sorted by model distance: nonbonded pdb=" O GLY A 56 " pdb="NA NA A 701 " model vdw 2.218 2.470 nonbonded pdb=" OH TYR A 320 " pdb=" OD2 ASP A 325 " model vdw 2.260 3.040 nonbonded pdb=" OD2 ASP A 494 " pdb=" OG1 THR A 596 " model vdw 2.302 3.040 nonbonded pdb=" OH TYR A 489 " pdb=" O GLY A 501 " model vdw 2.303 3.040 nonbonded pdb=" O PHE A 86 " pdb=" N GLY A 91 " model vdw 2.303 3.120 ... (remaining 38435 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 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: 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: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 3.560 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:4.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 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 : 0.005 0.047 4569 Z= 0.344 Angle : 0.784 6.024 6249 Z= 0.504 Chirality : 0.047 0.214 691 Planarity : 0.005 0.048 749 Dihedral : 15.251 81.553 1738 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.00 % Allowed : 20.13 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.35), residues: 538 helix: 0.56 (0.25), residues: 379 sheet: None (None), residues: 0 loop : -1.05 (0.49), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 177 TYR 0.011 0.001 TYR A 69 PHE 0.013 0.001 PHE A 58 TRP 0.016 0.001 TRP A 166 HIS 0.004 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00526 ( 4568) covalent geometry : angle 0.78369 ( 6247) SS BOND : bond 0.00024 ( 1) SS BOND : angle 1.60703 ( 2) hydrogen bonds : bond 0.21228 ( 284) hydrogen bonds : angle 7.82140 ( 834) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.087 Fit side-chains revert: symmetry clash REVERT: A 237 LYS cc_start: 0.6801 (mtpp) cc_final: 0.6040 (mmtt) REVERT: A 293 ASP cc_start: 0.8137 (m-30) cc_final: 0.7758 (m-30) REVERT: A 324 ARG cc_start: 0.7485 (mmt-90) cc_final: 0.7270 (mmt180) REVERT: A 364 GLU cc_start: 0.8490 (tt0) cc_final: 0.8137 (tt0) REVERT: A 378 VAL cc_start: 0.8679 (t) cc_final: 0.8097 (p) REVERT: A 383 LEU cc_start: 0.7989 (tp) cc_final: 0.7708 (mt) REVERT: A 495 MET cc_start: 0.8599 (mtp) cc_final: 0.8394 (mtp) REVERT: A 588 TRP cc_start: 0.7120 (m100) cc_final: 0.6826 (m100) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.2535 time to fit residues: 31.8097 Evaluate side-chains 77 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 0.1980 chunk 53 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.140966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.121291 restraints weight = 5075.010| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.28 r_work: 0.3227 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4569 Z= 0.162 Angle : 0.619 7.408 6249 Z= 0.309 Chirality : 0.043 0.271 691 Planarity : 0.005 0.034 749 Dihedral : 8.549 58.223 798 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 4.55 % Allowed : 17.75 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.37), residues: 538 helix: 1.28 (0.26), residues: 382 sheet: None (None), residues: 0 loop : -0.93 (0.52), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 66 TYR 0.012 0.002 TYR A 578 PHE 0.015 0.002 PHE A 392 TRP 0.015 0.002 TRP A 470 HIS 0.001 0.000 HIS A 164 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 4568) covalent geometry : angle 0.61864 ( 6247) SS BOND : bond 0.00038 ( 1) SS BOND : angle 0.82069 ( 2) hydrogen bonds : bond 0.04738 ( 284) hydrogen bonds : angle 5.16317 ( 834) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 74 time to evaluate : 0.087 Fit side-chains revert: symmetry clash REVERT: A 324 ARG cc_start: 0.7833 (mmt-90) cc_final: 0.7627 (mpt90) REVERT: A 383 LEU cc_start: 0.8291 (tp) cc_final: 0.8047 (mt) REVERT: A 526 LYS cc_start: 0.7669 (mtpt) cc_final: 0.7258 (mmtt) REVERT: A 587 ARG cc_start: 0.6951 (ptm-80) cc_final: 0.6330 (ptm-80) outliers start: 21 outliers final: 10 residues processed: 86 average time/residue: 0.2077 time to fit residues: 18.9152 Evaluate side-chains 77 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 593 GLU Chi-restraints excluded: chain A residue 596 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 9 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 20 optimal weight: 0.6980 chunk 34 optimal weight: 0.2980 chunk 46 optimal weight: 0.0070 chunk 27 optimal weight: 1.9990 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN A 586 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.136669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.117594 restraints weight = 5050.647| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.20 r_work: 0.3188 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4569 Z= 0.126 Angle : 0.545 6.499 6249 Z= 0.273 Chirality : 0.041 0.224 691 Planarity : 0.004 0.034 749 Dihedral : 8.069 59.715 798 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 4.76 % Allowed : 17.97 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.37), residues: 538 helix: 1.49 (0.26), residues: 381 sheet: None (None), residues: 0 loop : -1.00 (0.51), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 587 TYR 0.013 0.001 TYR A 578 PHE 0.013 0.001 PHE A 474 TRP 0.024 0.001 TRP A 588 HIS 0.001 0.000 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 4568) covalent geometry : angle 0.54491 ( 6247) SS BOND : bond 0.00047 ( 1) SS BOND : angle 1.03571 ( 2) hydrogen bonds : bond 0.04229 ( 284) hydrogen bonds : angle 4.86426 ( 834) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 73 time to evaluate : 0.111 Fit side-chains revert: symmetry clash REVERT: A 176 MET cc_start: 0.8329 (OUTLIER) cc_final: 0.7828 (mmt) REVERT: A 324 ARG cc_start: 0.7852 (mmt-90) cc_final: 0.7608 (mpt90) REVERT: A 380 MET cc_start: 0.8447 (mmm) cc_final: 0.8133 (mmp) REVERT: A 383 LEU cc_start: 0.8306 (tp) cc_final: 0.8089 (mt) REVERT: A 402 SER cc_start: 0.8924 (t) cc_final: 0.8651 (m) REVERT: A 495 MET cc_start: 0.8650 (mtp) cc_final: 0.8403 (mtp) REVERT: A 573 LEU cc_start: 0.5981 (OUTLIER) cc_final: 0.5759 (mm) REVERT: A 586 ASN cc_start: 0.7462 (OUTLIER) cc_final: 0.7028 (t160) REVERT: A 587 ARG cc_start: 0.6980 (ptm-80) cc_final: 0.6425 (ptm-80) REVERT: A 588 TRP cc_start: 0.7441 (m100) cc_final: 0.7007 (m100) outliers start: 22 outliers final: 8 residues processed: 86 average time/residue: 0.2428 time to fit residues: 21.9703 Evaluate side-chains 74 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 586 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 0 optimal weight: 8.9990 chunk 3 optimal weight: 0.7980 chunk 6 optimal weight: 0.3980 chunk 39 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.134314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.115276 restraints weight = 5018.588| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.22 r_work: 0.3167 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4569 Z= 0.145 Angle : 0.564 6.576 6249 Z= 0.281 Chirality : 0.042 0.224 691 Planarity : 0.004 0.035 749 Dihedral : 7.968 59.680 798 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 5.19 % Allowed : 17.32 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.36), residues: 538 helix: 1.49 (0.26), residues: 380 sheet: None (None), residues: 0 loop : -1.07 (0.50), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 587 TYR 0.013 0.001 TYR A 578 PHE 0.017 0.002 PHE A 386 TRP 0.015 0.001 TRP A 470 HIS 0.001 0.000 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 4568) covalent geometry : angle 0.56340 ( 6247) SS BOND : bond 0.00014 ( 1) SS BOND : angle 1.13006 ( 2) hydrogen bonds : bond 0.04161 ( 284) hydrogen bonds : angle 4.87024 ( 834) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 65 time to evaluate : 0.090 Fit side-chains revert: symmetry clash REVERT: A 176 MET cc_start: 0.8352 (OUTLIER) cc_final: 0.7844 (mmt) REVERT: A 380 MET cc_start: 0.8510 (mmm) cc_final: 0.8150 (mmp) REVERT: A 383 LEU cc_start: 0.8224 (tp) cc_final: 0.8008 (mt) REVERT: A 402 SER cc_start: 0.8924 (t) cc_final: 0.8669 (m) REVERT: A 429 GLU cc_start: 0.7174 (pt0) cc_final: 0.6921 (pt0) REVERT: A 514 VAL cc_start: 0.8734 (OUTLIER) cc_final: 0.8426 (t) REVERT: A 587 ARG cc_start: 0.6943 (ptm-80) cc_final: 0.6467 (ptm-80) REVERT: A 588 TRP cc_start: 0.7385 (m100) cc_final: 0.6385 (m100) REVERT: A 592 ARG cc_start: 0.5234 (OUTLIER) cc_final: 0.3742 (mpt-90) REVERT: A 596 THR cc_start: 0.8357 (OUTLIER) cc_final: 0.8028 (t) outliers start: 24 outliers final: 12 residues processed: 81 average time/residue: 0.2610 time to fit residues: 22.2180 Evaluate side-chains 76 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 504 MET Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 592 ARG Chi-restraints excluded: chain A residue 593 GLU Chi-restraints excluded: chain A residue 596 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 34 optimal weight: 0.9990 chunk 1 optimal weight: 0.0870 chunk 49 optimal weight: 0.0270 chunk 4 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 overall best weight: 0.4416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.140947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.121959 restraints weight = 5079.247| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.28 r_work: 0.3262 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4569 Z= 0.119 Angle : 0.542 8.077 6249 Z= 0.268 Chirality : 0.040 0.211 691 Planarity : 0.004 0.034 749 Dihedral : 7.695 59.695 798 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 4.98 % Allowed : 17.32 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.37), residues: 538 helix: 1.60 (0.26), residues: 380 sheet: None (None), residues: 0 loop : -1.04 (0.51), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 66 TYR 0.015 0.001 TYR A 578 PHE 0.015 0.001 PHE A 386 TRP 0.018 0.001 TRP A 470 HIS 0.001 0.000 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 4568) covalent geometry : angle 0.54132 ( 6247) SS BOND : bond 0.00052 ( 1) SS BOND : angle 1.07368 ( 2) hydrogen bonds : bond 0.03837 ( 284) hydrogen bonds : angle 4.70643 ( 834) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 63 time to evaluate : 0.086 Fit side-chains revert: symmetry clash REVERT: A 176 MET cc_start: 0.8365 (OUTLIER) cc_final: 0.7880 (mmt) REVERT: A 237 LYS cc_start: 0.6888 (OUTLIER) cc_final: 0.5854 (mmmt) REVERT: A 380 MET cc_start: 0.8461 (mmm) cc_final: 0.8140 (mmp) REVERT: A 514 VAL cc_start: 0.8726 (OUTLIER) cc_final: 0.8425 (t) REVERT: A 587 ARG cc_start: 0.6953 (ptm-80) cc_final: 0.6408 (ptm-80) REVERT: A 596 THR cc_start: 0.8289 (OUTLIER) cc_final: 0.7987 (t) outliers start: 23 outliers final: 9 residues processed: 77 average time/residue: 0.2704 time to fit residues: 21.7810 Evaluate side-chains 69 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 237 LYS Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 504 MET Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 593 GLU Chi-restraints excluded: chain A residue 596 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 18 optimal weight: 5.9990 chunk 7 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 26 optimal weight: 0.4980 chunk 29 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 44 optimal weight: 0.3980 chunk 21 optimal weight: 1.9990 chunk 10 optimal weight: 0.0670 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN A 567 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.141113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.121665 restraints weight = 5180.420| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.34 r_work: 0.3267 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4569 Z= 0.120 Angle : 0.540 8.298 6249 Z= 0.267 Chirality : 0.040 0.209 691 Planarity : 0.004 0.033 749 Dihedral : 7.535 59.697 798 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 4.55 % Allowed : 18.83 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.37), residues: 538 helix: 1.61 (0.27), residues: 382 sheet: None (None), residues: 0 loop : -0.98 (0.51), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 324 TYR 0.018 0.001 TYR A 578 PHE 0.014 0.001 PHE A 386 TRP 0.016 0.001 TRP A 588 HIS 0.001 0.000 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 4568) covalent geometry : angle 0.53931 ( 6247) SS BOND : bond 0.00044 ( 1) SS BOND : angle 1.07034 ( 2) hydrogen bonds : bond 0.03762 ( 284) hydrogen bonds : angle 4.63004 ( 834) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 59 time to evaluate : 0.087 Fit side-chains revert: symmetry clash REVERT: A 176 MET cc_start: 0.8373 (OUTLIER) cc_final: 0.7818 (mmt) REVERT: A 237 LYS cc_start: 0.6890 (OUTLIER) cc_final: 0.5842 (mmmt) REVERT: A 324 ARG cc_start: 0.7481 (mpt90) cc_final: 0.7064 (mmm160) REVERT: A 364 GLU cc_start: 0.8626 (tt0) cc_final: 0.8229 (tt0) REVERT: A 380 MET cc_start: 0.8473 (mmm) cc_final: 0.8153 (mmp) REVERT: A 514 VAL cc_start: 0.8663 (OUTLIER) cc_final: 0.8376 (t) REVERT: A 596 THR cc_start: 0.8277 (OUTLIER) cc_final: 0.7987 (t) outliers start: 21 outliers final: 11 residues processed: 71 average time/residue: 0.2733 time to fit residues: 20.3127 Evaluate side-chains 74 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 237 LYS Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 504 MET Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 593 GLU Chi-restraints excluded: chain A residue 596 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 33 optimal weight: 1.9990 chunk 38 optimal weight: 0.4980 chunk 2 optimal weight: 0.2980 chunk 16 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 chunk 22 optimal weight: 0.0370 chunk 18 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 567 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.140742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.121535 restraints weight = 5098.068| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.34 r_work: 0.3245 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4569 Z= 0.117 Angle : 0.540 8.778 6249 Z= 0.267 Chirality : 0.040 0.206 691 Planarity : 0.004 0.033 749 Dihedral : 7.418 59.444 798 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 4.33 % Allowed : 19.26 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.37), residues: 538 helix: 1.68 (0.27), residues: 382 sheet: None (None), residues: 0 loop : -1.00 (0.50), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 587 TYR 0.018 0.001 TYR A 578 PHE 0.013 0.001 PHE A 434 TRP 0.016 0.001 TRP A 470 HIS 0.001 0.000 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 4568) covalent geometry : angle 0.53970 ( 6247) SS BOND : bond 0.00060 ( 1) SS BOND : angle 1.10865 ( 2) hydrogen bonds : bond 0.03683 ( 284) hydrogen bonds : angle 4.63108 ( 834) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 57 time to evaluate : 0.086 Fit side-chains revert: symmetry clash REVERT: A 176 MET cc_start: 0.8390 (OUTLIER) cc_final: 0.7833 (mmt) REVERT: A 237 LYS cc_start: 0.6901 (OUTLIER) cc_final: 0.5824 (mmmt) REVERT: A 324 ARG cc_start: 0.7502 (mpt90) cc_final: 0.7065 (mmm160) REVERT: A 364 GLU cc_start: 0.8641 (tt0) cc_final: 0.8234 (tt0) REVERT: A 380 MET cc_start: 0.8461 (mmm) cc_final: 0.8139 (mmp) REVERT: A 514 VAL cc_start: 0.8652 (OUTLIER) cc_final: 0.8360 (t) REVERT: A 587 ARG cc_start: 0.6919 (ttp-110) cc_final: 0.6518 (ptm-80) REVERT: A 596 THR cc_start: 0.8252 (OUTLIER) cc_final: 0.7946 (t) outliers start: 20 outliers final: 11 residues processed: 68 average time/residue: 0.2558 time to fit residues: 18.2448 Evaluate side-chains 71 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 237 LYS Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 504 MET Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 596 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 36 optimal weight: 0.7980 chunk 46 optimal weight: 0.1980 chunk 24 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 10 optimal weight: 0.0070 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 ASN A 567 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.141935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.122421 restraints weight = 5085.857| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.36 r_work: 0.3278 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4569 Z= 0.116 Angle : 0.535 8.047 6249 Z= 0.263 Chirality : 0.040 0.204 691 Planarity : 0.004 0.032 749 Dihedral : 7.279 59.304 798 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.46 % Allowed : 20.13 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.37), residues: 538 helix: 1.77 (0.27), residues: 382 sheet: None (None), residues: 0 loop : -1.02 (0.50), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 587 TYR 0.020 0.001 TYR A 578 PHE 0.012 0.001 PHE A 386 TRP 0.016 0.001 TRP A 470 HIS 0.001 0.000 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 4568) covalent geometry : angle 0.53488 ( 6247) SS BOND : bond 0.00042 ( 1) SS BOND : angle 1.11293 ( 2) hydrogen bonds : bond 0.03635 ( 284) hydrogen bonds : angle 4.54766 ( 834) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.083 Fit side-chains revert: symmetry clash REVERT: A 176 MET cc_start: 0.8371 (OUTLIER) cc_final: 0.7821 (mmt) REVERT: A 237 LYS cc_start: 0.6892 (OUTLIER) cc_final: 0.6120 (mmtt) REVERT: A 324 ARG cc_start: 0.7540 (mpt90) cc_final: 0.7050 (mmm160) REVERT: A 364 GLU cc_start: 0.8608 (tt0) cc_final: 0.8295 (tt0) REVERT: A 380 MET cc_start: 0.8449 (mmm) cc_final: 0.8127 (mmp) REVERT: A 446 MET cc_start: 0.9176 (mtm) cc_final: 0.8843 (mtm) REVERT: A 514 VAL cc_start: 0.8638 (OUTLIER) cc_final: 0.8360 (t) REVERT: A 587 ARG cc_start: 0.6883 (ttp-110) cc_final: 0.6545 (ptm-80) REVERT: A 596 THR cc_start: 0.8199 (p) cc_final: 0.7912 (t) outliers start: 16 outliers final: 12 residues processed: 69 average time/residue: 0.2569 time to fit residues: 18.5890 Evaluate side-chains 72 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 237 LYS Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 504 MET Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 574 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 22 optimal weight: 1.9990 chunk 36 optimal weight: 0.0170 chunk 15 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 47 optimal weight: 0.0270 chunk 0 optimal weight: 8.9990 chunk 17 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 overall best weight: 0.4876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 567 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.141672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.122074 restraints weight = 5110.748| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.37 r_work: 0.3263 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4569 Z= 0.120 Angle : 0.548 9.807 6249 Z= 0.268 Chirality : 0.040 0.204 691 Planarity : 0.004 0.032 749 Dihedral : 7.238 59.652 798 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.68 % Allowed : 20.56 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.37), residues: 538 helix: 1.74 (0.27), residues: 383 sheet: None (None), residues: 0 loop : -1.01 (0.50), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 587 TYR 0.021 0.001 TYR A 578 PHE 0.012 0.001 PHE A 386 TRP 0.014 0.001 TRP A 470 HIS 0.001 0.000 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 4568) covalent geometry : angle 0.54734 ( 6247) SS BOND : bond 0.00068 ( 1) SS BOND : angle 1.15917 ( 2) hydrogen bonds : bond 0.03631 ( 284) hydrogen bonds : angle 4.56409 ( 834) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 58 time to evaluate : 0.085 Fit side-chains revert: symmetry clash REVERT: A 176 MET cc_start: 0.8400 (OUTLIER) cc_final: 0.7842 (mmt) REVERT: A 237 LYS cc_start: 0.6944 (OUTLIER) cc_final: 0.6212 (mmtt) REVERT: A 324 ARG cc_start: 0.7667 (mpt90) cc_final: 0.7143 (mmm160) REVERT: A 364 GLU cc_start: 0.8644 (tt0) cc_final: 0.8344 (tt0) REVERT: A 380 MET cc_start: 0.8455 (mmm) cc_final: 0.8126 (mmp) REVERT: A 514 VAL cc_start: 0.8649 (OUTLIER) cc_final: 0.8368 (t) REVERT: A 587 ARG cc_start: 0.6892 (ttp-110) cc_final: 0.6551 (ptm-80) REVERT: A 596 THR cc_start: 0.8224 (p) cc_final: 0.7931 (t) outliers start: 17 outliers final: 12 residues processed: 67 average time/residue: 0.2569 time to fit residues: 18.0500 Evaluate side-chains 72 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 237 LYS Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 504 MET Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 574 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 51 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 6 optimal weight: 0.0980 chunk 36 optimal weight: 0.0370 chunk 17 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 33 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.5660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 567 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.139930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.121171 restraints weight = 5126.167| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.29 r_work: 0.3252 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4569 Z= 0.127 Angle : 0.555 9.299 6249 Z= 0.272 Chirality : 0.040 0.205 691 Planarity : 0.004 0.033 749 Dihedral : 7.235 59.946 798 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.90 % Allowed : 20.35 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.37), residues: 538 helix: 1.73 (0.27), residues: 383 sheet: None (None), residues: 0 loop : -0.98 (0.51), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 587 TYR 0.024 0.001 TYR A 578 PHE 0.012 0.001 PHE A 392 TRP 0.016 0.001 TRP A 218 HIS 0.001 0.000 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 4568) covalent geometry : angle 0.55428 ( 6247) SS BOND : bond 0.00069 ( 1) SS BOND : angle 1.20360 ( 2) hydrogen bonds : bond 0.03698 ( 284) hydrogen bonds : angle 4.57726 ( 834) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 60 time to evaluate : 0.084 Fit side-chains revert: symmetry clash REVERT: A 176 MET cc_start: 0.8439 (OUTLIER) cc_final: 0.7913 (mmt) REVERT: A 237 LYS cc_start: 0.6943 (OUTLIER) cc_final: 0.6229 (mmtt) REVERT: A 324 ARG cc_start: 0.7670 (mpt90) cc_final: 0.7213 (mmm160) REVERT: A 380 MET cc_start: 0.8465 (mmm) cc_final: 0.8141 (mmp) REVERT: A 514 VAL cc_start: 0.8661 (OUTLIER) cc_final: 0.8384 (t) REVERT: A 587 ARG cc_start: 0.6899 (ttp-110) cc_final: 0.6568 (ptm-80) REVERT: A 596 THR cc_start: 0.8275 (p) cc_final: 0.7986 (t) outliers start: 18 outliers final: 12 residues processed: 70 average time/residue: 0.2575 time to fit residues: 18.8986 Evaluate side-chains 75 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 237 LYS Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 504 MET Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 574 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 23 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 12 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 24 optimal weight: 0.0060 chunk 19 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 30 optimal weight: 0.0470 chunk 27 optimal weight: 0.9980 overall best weight: 0.5094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 567 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.141114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.121887 restraints weight = 5124.964| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.32 r_work: 0.3255 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4569 Z= 0.122 Angle : 0.548 9.125 6249 Z= 0.270 Chirality : 0.040 0.203 691 Planarity : 0.004 0.032 749 Dihedral : 7.196 59.770 798 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.46 % Allowed : 20.56 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.37), residues: 538 helix: 1.72 (0.27), residues: 385 sheet: None (None), residues: 0 loop : -1.00 (0.51), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 587 TYR 0.024 0.001 TYR A 578 PHE 0.012 0.001 PHE A 386 TRP 0.015 0.001 TRP A 218 HIS 0.001 0.000 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 4568) covalent geometry : angle 0.54785 ( 6247) SS BOND : bond 0.00064 ( 1) SS BOND : angle 1.19828 ( 2) hydrogen bonds : bond 0.03661 ( 284) hydrogen bonds : angle 4.56592 ( 834) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 933.03 seconds wall clock time: 18 minutes 26.36 seconds (1106.36 seconds total)