Starting phenix.real_space_refine on Fri Aug 22 14:02:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mc8_63792/08_2025/9mc8_63792_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mc8_63792/08_2025/9mc8_63792.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mc8_63792/08_2025/9mc8_63792_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mc8_63792/08_2025/9mc8_63792_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mc8_63792/08_2025/9mc8_63792.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mc8_63792/08_2025/9mc8_63792.map" } resolution = 3.31 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= 0.000 sd= 0.074 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 2422 2.51 5 N 620 2.21 5 O 649 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3721 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3693 Classifications: {'peptide': 489} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 26, 'TRANS': 462} Chain breaks: 3 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'TRP:plan': 1, 'ARG:plan': 7, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 72 Chain: "A" Number of atoms: 28 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1, 14 Unusual residues: {'ZWD': 1} Classifications: {'undetermined': 1} Conformer: "B" Number of residues, atoms: 1, 14 Unusual residues: {'ZWD': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C01AZWD A 601 " occ=0.50 ... (26 atoms not shown) pdb=" O13BZWD A 601 " occ=0.50 Time building chain proxies: 1.17, per 1000 atoms: 0.31 Number of scatterers: 3721 At special positions: 0 Unit cell: (98.792, 54.056, 67.104, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 649 8.00 N 620 7.00 C 2422 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 105 " distance=2.03 Simple disulfide: pdb=" SG CYS A 78 " - pdb=" SG CYS A 128 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 0.33 Conformation dependent library (CDL) restraints added in 157.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 962 Ramachandran restraints generated. 481 Oldfield, 0 Emsley, 481 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 906 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 0 sheets defined 81.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 3 through 10 Processing helix chain 'A' and resid 14 through 26 Processing helix chain 'A' and resid 27 through 29 No H-bonds generated for 'chain 'A' and resid 27 through 29' Processing helix chain 'A' and resid 30 through 36 Processing helix chain 'A' and resid 37 through 40 Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 127 through 130 Processing helix chain 'A' and resid 131 through 160 removed outlier: 4.195A pdb=" N GLN A 135 " --> pdb=" O ARG A 131 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN A 138 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE A 152 " --> pdb=" O GLY A 148 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY A 153 " --> pdb=" O ALA A 149 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY A 160 " --> pdb=" O ALA A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 181 Processing helix chain 'A' and resid 184 through 214 removed outlier: 3.553A pdb=" N MET A 207 " --> pdb=" O SER A 203 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TRP A 213 " --> pdb=" O LEU A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 217 No H-bonds generated for 'chain 'A' and resid 215 through 217' Processing helix chain 'A' and resid 218 through 244 removed outlier: 3.591A pdb=" N GLN A 234 " --> pdb=" O TYR A 230 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR A 242 " --> pdb=" O ALA A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 256 Processing helix chain 'A' and resid 256 through 265 removed outlier: 3.902A pdb=" N ALA A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 271 through 279 Processing helix chain 'A' and resid 280 through 295 Processing helix chain 'A' and resid 297 through 304 removed outlier: 3.520A pdb=" N GLY A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 314 Processing helix chain 'A' and resid 326 through 332 removed outlier: 3.838A pdb=" N LEU A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 358 removed outlier: 3.628A pdb=" N LEU A 338 " --> pdb=" O THR A 334 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N MET A 358 " --> pdb=" O TYR A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 364 removed outlier: 3.902A pdb=" N PHE A 363 " --> pdb=" O LEU A 360 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY A 364 " --> pdb=" O GLN A 361 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 360 through 364' Processing helix chain 'A' and resid 366 through 392 removed outlier: 3.978A pdb=" N ASP A 378 " --> pdb=" O PHE A 374 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N LEU A 379 " --> pdb=" O GLY A 375 " (cutoff:3.500A) Proline residue: A 380 - end of helix removed outlier: 3.593A pdb=" N LEU A 383 " --> pdb=" O LEU A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 415 Processing helix chain 'A' and resid 419 through 449 removed outlier: 3.654A pdb=" N ARG A 423 " --> pdb=" O GLN A 419 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TYR A 449 " --> pdb=" O THR A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 478 Proline residue: A 473 - end of helix removed outlier: 3.825A pdb=" N THR A 478 " --> pdb=" O LEU A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 481 No H-bonds generated for 'chain 'A' and resid 479 through 481' Processing helix chain 'A' and resid 484 through 502 Proline residue: A 494 - end of helix removed outlier: 3.930A pdb=" N VAL A 502 " --> pdb=" O SER A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 522 258 hydrogen bonds defined for protein. 768 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: 0.60 Time building geometry restraints manager: 0.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 771 1.33 - 1.45: 867 1.45 - 1.57: 2121 1.57 - 1.69: 1 1.69 - 1.82: 47 Bond restraints: 3807 Sorted by residual: bond pdb=" C11AZWD A 601 " pdb=" O13AZWD A 601 " ideal model delta sigma weight residual 1.255 1.351 -0.096 2.00e-02 2.50e+03 2.28e+01 bond pdb=" C11BZWD A 601 " pdb=" O13BZWD A 601 " ideal model delta sigma weight residual 1.255 1.346 -0.091 2.00e-02 2.50e+03 2.07e+01 bond pdb=" C11BZWD A 601 " pdb=" O12BZWD A 601 " ideal model delta sigma weight residual 1.255 1.207 0.048 2.00e-02 2.50e+03 5.71e+00 bond pdb=" CB PRO A 52 " pdb=" CG PRO A 52 " ideal model delta sigma weight residual 1.492 1.607 -0.115 5.00e-02 4.00e+02 5.27e+00 bond pdb=" C11AZWD A 601 " pdb=" O12AZWD A 601 " ideal model delta sigma weight residual 1.255 1.209 0.046 2.00e-02 2.50e+03 5.25e+00 ... (remaining 3802 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 5000 1.99 - 3.98: 158 3.98 - 5.98: 19 5.98 - 7.97: 9 7.97 - 9.96: 4 Bond angle restraints: 5190 Sorted by residual: angle pdb=" CA PRO A 52 " pdb=" N PRO A 52 " pdb=" CD PRO A 52 " ideal model delta sigma weight residual 112.00 105.64 6.36 1.40e+00 5.10e-01 2.06e+01 angle pdb=" N GLY A 73 " pdb=" CA GLY A 73 " pdb=" C GLY A 73 " ideal model delta sigma weight residual 114.69 109.79 4.90 1.19e+00 7.06e-01 1.70e+01 angle pdb=" N THR A 82 " pdb=" CA THR A 82 " pdb=" C THR A 82 " ideal model delta sigma weight residual 111.28 106.81 4.47 1.09e+00 8.42e-01 1.68e+01 angle pdb=" C ILE A 110 " pdb=" CA ILE A 110 " pdb=" CB ILE A 110 " ideal model delta sigma weight residual 113.22 108.90 4.32 1.12e+00 7.97e-01 1.48e+01 angle pdb=" C GLN A 510 " pdb=" N PRO A 511 " pdb=" CA PRO A 511 " ideal model delta sigma weight residual 120.03 116.28 3.75 9.90e-01 1.02e+00 1.43e+01 ... (remaining 5185 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.07: 1985 17.07 - 34.15: 200 34.15 - 51.22: 41 51.22 - 68.29: 11 68.29 - 85.37: 6 Dihedral angle restraints: 2243 sinusoidal: 836 harmonic: 1407 Sorted by residual: dihedral pdb=" CB GLU A 270 " pdb=" CG GLU A 270 " pdb=" CD GLU A 270 " pdb=" OE1 GLU A 270 " ideal model delta sinusoidal sigma weight residual 0.00 85.30 -85.30 1 3.00e+01 1.11e-03 9.79e+00 dihedral pdb=" CA PHE A 152 " pdb=" C PHE A 152 " pdb=" N GLY A 153 " pdb=" CA GLY A 153 " ideal model delta harmonic sigma weight residual 180.00 164.58 15.42 0 5.00e+00 4.00e-02 9.51e+00 dihedral pdb=" CA GLN A 135 " pdb=" CB GLN A 135 " pdb=" CG GLN A 135 " pdb=" CD GLN A 135 " ideal model delta sinusoidal sigma weight residual 60.00 117.63 -57.63 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 2240 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 343 0.026 - 0.053: 167 0.053 - 0.079: 69 0.079 - 0.106: 27 0.106 - 0.132: 8 Chirality restraints: 614 Sorted by residual: chirality pdb=" CB ILE A 409 " pdb=" CA ILE A 409 " pdb=" CG1 ILE A 409 " pdb=" CG2 ILE A 409 " both_signs ideal model delta sigma weight residual False 2.64 2.78 -0.13 2.00e-01 2.50e+01 4.37e-01 chirality pdb=" CA CYS A 78 " pdb=" N CYS A 78 " pdb=" C CYS A 78 " pdb=" CB CYS A 78 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.15e-01 chirality pdb=" CA LEU A 356 " pdb=" N LEU A 356 " pdb=" C LEU A 356 " pdb=" CB LEU A 356 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.56e-01 ... (remaining 611 not shown) Planarity restraints: 651 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 51 " 0.063 5.00e-02 4.00e+02 9.30e-02 1.38e+01 pdb=" N PRO A 52 " -0.161 5.00e-02 4.00e+02 pdb=" CA PRO A 52 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 52 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 482 " -0.044 5.00e-02 4.00e+02 6.77e-02 7.33e+00 pdb=" N PRO A 483 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 483 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 483 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 256 " -0.043 5.00e-02 4.00e+02 6.53e-02 6.82e+00 pdb=" N PRO A 257 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 257 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 257 " -0.036 5.00e-02 4.00e+02 ... (remaining 648 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 1412 2.86 - 3.37: 4003 3.37 - 3.88: 6304 3.88 - 4.39: 7112 4.39 - 4.90: 11787 Nonbonded interactions: 30618 Sorted by model distance: nonbonded pdb=" OE1 GLU A 212 " pdb=" OG SER A 271 " model vdw 2.353 3.040 nonbonded pdb=" O SER A 472 " pdb=" OH TYR A 490 " model vdw 2.422 3.040 nonbonded pdb=" O CYS A 221 " pdb=" OG1 THR A 224 " model vdw 2.426 3.040 nonbonded pdb=" N GLU A 316 " pdb=" OE1 GLU A 316 " model vdw 2.439 3.120 nonbonded pdb=" NE2 GLN A 17 " pdb=" O TRP A 213 " model vdw 2.445 3.120 ... (remaining 30613 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=0.50 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: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.870 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6407 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 0.115 3809 Z= 0.280 Angle : 0.854 9.960 5194 Z= 0.483 Chirality : 0.039 0.132 614 Planarity : 0.008 0.093 651 Dihedral : 15.337 85.368 1331 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.26 % Allowed : 14.14 % Favored : 85.60 % 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 aren not related in a simple way. whole: 0.19 (0.40), residues: 481 helix: 0.36 (0.28), residues: 363 sheet: -1.01 (2.07), residues: 10 loop : -0.07 (0.67), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 394 TYR 0.010 0.001 TYR A 230 PHE 0.025 0.002 PHE A 386 TRP 0.013 0.001 TRP A 274 HIS 0.006 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00541 ( 3807) covalent geometry : angle 0.85463 ( 5190) SS BOND : bond 0.00426 ( 2) SS BOND : angle 0.27789 ( 4) hydrogen bonds : bond 0.16200 ( 258) hydrogen bonds : angle 7.00359 ( 768) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 962 Ramachandran restraints generated. 481 Oldfield, 0 Emsley, 481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 962 Ramachandran restraints generated. 481 Oldfield, 0 Emsley, 481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 89 time to evaluate : 0.166 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 THR cc_start: 0.8459 (m) cc_final: 0.8178 (p) REVERT: A 510 GLN cc_start: 0.7417 (mm110) cc_final: 0.6570 (tt0) outliers start: 1 outliers final: 0 residues processed: 90 average time/residue: 0.0496 time to fit residues: 6.0361 Evaluate side-chains 76 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN A 439 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.171062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.134864 restraints weight = 4652.186| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 2.68 r_work: 0.3563 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3618 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3618 r_free = 0.3618 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3618 r_free = 0.3618 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3618 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3809 Z= 0.156 Angle : 0.611 6.931 5194 Z= 0.295 Chirality : 0.039 0.126 614 Planarity : 0.006 0.063 651 Dihedral : 9.222 88.366 536 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 3.08 % Allowed : 14.14 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.61 (0.39), residues: 481 helix: 1.22 (0.27), residues: 362 sheet: -1.59 (1.63), residues: 10 loop : 1.21 (0.68), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 466 TYR 0.008 0.001 TYR A 111 PHE 0.017 0.002 PHE A 351 TRP 0.013 0.001 TRP A 274 HIS 0.004 0.001 HIS A 217 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 3807) covalent geometry : angle 0.61071 ( 5190) SS BOND : bond 0.00314 ( 2) SS BOND : angle 0.41551 ( 4) hydrogen bonds : bond 0.04696 ( 258) hydrogen bonds : angle 4.37240 ( 768) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 962 Ramachandran restraints generated. 481 Oldfield, 0 Emsley, 481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 962 Ramachandran restraints generated. 481 Oldfield, 0 Emsley, 481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.139 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 GLN cc_start: 0.8658 (tp-100) cc_final: 0.8006 (tp-100) REVERT: A 142 MET cc_start: 0.8032 (mmm) cc_final: 0.7598 (mmt) REVERT: A 403 LEU cc_start: 0.7813 (tt) cc_final: 0.7576 (tp) outliers start: 12 outliers final: 9 residues processed: 86 average time/residue: 0.0362 time to fit residues: 4.4024 Evaluate side-chains 87 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 507 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 14 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 4 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.169436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.132358 restraints weight = 4567.589| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 2.70 r_work: 0.3540 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3571 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3571 r_free = 0.3571 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3571 r_free = 0.3571 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3571 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3809 Z= 0.151 Angle : 0.571 5.524 5194 Z= 0.279 Chirality : 0.038 0.126 614 Planarity : 0.006 0.061 651 Dihedral : 9.001 89.911 536 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 4.11 % Allowed : 14.14 % Favored : 81.75 % 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 aren not related in a simple way. whole: 2.17 (0.39), residues: 481 helix: 1.59 (0.27), residues: 360 sheet: -1.67 (1.52), residues: 10 loop : 1.61 (0.70), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 466 TYR 0.007 0.001 TYR A 111 PHE 0.017 0.001 PHE A 351 TRP 0.012 0.001 TRP A 274 HIS 0.003 0.001 HIS A 217 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 3807) covalent geometry : angle 0.57142 ( 5190) SS BOND : bond 0.00352 ( 2) SS BOND : angle 0.34450 ( 4) hydrogen bonds : bond 0.04339 ( 258) hydrogen bonds : angle 4.14885 ( 768) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 962 Ramachandran restraints generated. 481 Oldfield, 0 Emsley, 481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 962 Ramachandran restraints generated. 481 Oldfield, 0 Emsley, 481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.178 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 GLN cc_start: 0.8596 (tp-100) cc_final: 0.8104 (tp-100) REVERT: A 358 MET cc_start: 0.7069 (mmm) cc_final: 0.6396 (mmm) outliers start: 16 outliers final: 12 residues processed: 85 average time/residue: 0.0427 time to fit residues: 5.0580 Evaluate side-chains 87 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 502 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 31 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 12 optimal weight: 0.4980 chunk 36 optimal weight: 1.9990 chunk 45 optimal weight: 0.0980 chunk 20 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.170251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.132624 restraints weight = 4635.044| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.72 r_work: 0.3546 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3576 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3576 r_free = 0.3576 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3576 r_free = 0.3576 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3576 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3809 Z= 0.128 Angle : 0.539 6.641 5194 Z= 0.265 Chirality : 0.037 0.126 614 Planarity : 0.005 0.059 651 Dihedral : 8.773 89.340 536 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.86 % Allowed : 16.20 % Favored : 79.95 % 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 aren not related in a simple way. whole: 2.48 (0.39), residues: 481 helix: 1.84 (0.27), residues: 360 sheet: -1.79 (1.47), residues: 10 loop : 1.66 (0.70), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 466 TYR 0.007 0.001 TYR A 354 PHE 0.016 0.001 PHE A 351 TRP 0.010 0.001 TRP A 274 HIS 0.006 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 3807) covalent geometry : angle 0.53922 ( 5190) SS BOND : bond 0.00299 ( 2) SS BOND : angle 0.32109 ( 4) hydrogen bonds : bond 0.03991 ( 258) hydrogen bonds : angle 3.96466 ( 768) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 962 Ramachandran restraints generated. 481 Oldfield, 0 Emsley, 481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 962 Ramachandran restraints generated. 481 Oldfield, 0 Emsley, 481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.149 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 GLN cc_start: 0.8579 (tp-100) cc_final: 0.8147 (tp-100) REVERT: A 386 PHE cc_start: 0.7818 (t80) cc_final: 0.7380 (t80) REVERT: A 390 ASN cc_start: 0.7083 (m-40) cc_final: 0.6840 (m-40) REVERT: A 438 PHE cc_start: 0.7994 (OUTLIER) cc_final: 0.7633 (t80) outliers start: 15 outliers final: 11 residues processed: 86 average time/residue: 0.0399 time to fit residues: 4.8701 Evaluate side-chains 87 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ASN Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 507 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 39 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 15 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.169749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.131870 restraints weight = 4640.549| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 2.72 r_work: 0.3534 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3566 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3566 r_free = 0.3566 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3566 r_free = 0.3566 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3566 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3809 Z= 0.134 Angle : 0.553 5.854 5194 Z= 0.270 Chirality : 0.037 0.127 614 Planarity : 0.005 0.058 651 Dihedral : 8.553 86.824 536 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 4.11 % Allowed : 16.45 % Favored : 79.43 % 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 aren not related in a simple way. whole: 2.53 (0.39), residues: 481 helix: 1.90 (0.27), residues: 360 sheet: -1.75 (1.46), residues: 10 loop : 1.55 (0.69), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 466 TYR 0.007 0.001 TYR A 354 PHE 0.017 0.001 PHE A 351 TRP 0.009 0.001 TRP A 274 HIS 0.006 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 3807) covalent geometry : angle 0.55324 ( 5190) SS BOND : bond 0.00307 ( 2) SS BOND : angle 0.36368 ( 4) hydrogen bonds : bond 0.03930 ( 258) hydrogen bonds : angle 3.90523 ( 768) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 962 Ramachandran restraints generated. 481 Oldfield, 0 Emsley, 481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 962 Ramachandran restraints generated. 481 Oldfield, 0 Emsley, 481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.126 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 206 CYS cc_start: 0.7160 (OUTLIER) cc_final: 0.6702 (t) REVERT: A 358 MET cc_start: 0.6892 (mmm) cc_final: 0.6314 (mmm) REVERT: A 390 ASN cc_start: 0.7063 (m-40) cc_final: 0.6806 (m-40) REVERT: A 438 PHE cc_start: 0.8000 (OUTLIER) cc_final: 0.7668 (t80) REVERT: A 458 MET cc_start: 0.8121 (tpp) cc_final: 0.7916 (mmm) outliers start: 16 outliers final: 13 residues processed: 88 average time/residue: 0.0411 time to fit residues: 5.1349 Evaluate side-chains 90 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 HIS Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 502 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 15 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 45 optimal weight: 0.0670 chunk 7 optimal weight: 0.3980 chunk 39 optimal weight: 0.9980 chunk 0 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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 = 0.4123 r_free = 0.4123 target = 0.170585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.132584 restraints weight = 4705.521| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 2.75 r_work: 0.3546 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3572 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3572 r_free = 0.3572 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3572 r_free = 0.3572 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3572 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3809 Z= 0.130 Angle : 0.557 7.746 5194 Z= 0.271 Chirality : 0.038 0.145 614 Planarity : 0.005 0.057 651 Dihedral : 8.052 80.631 536 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 4.37 % Allowed : 16.20 % Favored : 79.43 % 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 aren not related in a simple way. whole: 2.61 (0.39), residues: 481 helix: 1.99 (0.27), residues: 360 sheet: -1.68 (1.55), residues: 10 loop : 1.43 (0.68), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 466 TYR 0.013 0.001 TYR A 169 PHE 0.017 0.001 PHE A 351 TRP 0.008 0.001 TRP A 274 HIS 0.005 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 3807) covalent geometry : angle 0.55701 ( 5190) SS BOND : bond 0.00291 ( 2) SS BOND : angle 0.37324 ( 4) hydrogen bonds : bond 0.03831 ( 258) hydrogen bonds : angle 3.82270 ( 768) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 962 Ramachandran restraints generated. 481 Oldfield, 0 Emsley, 481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 962 Ramachandran restraints generated. 481 Oldfield, 0 Emsley, 481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.178 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 GLN cc_start: 0.8873 (tm-30) cc_final: 0.8624 (tm-30) REVERT: A 206 CYS cc_start: 0.7150 (OUTLIER) cc_final: 0.6736 (t) REVERT: A 358 MET cc_start: 0.7050 (mmm) cc_final: 0.6402 (mmm) REVERT: A 390 ASN cc_start: 0.7068 (m-40) cc_final: 0.6709 (m-40) REVERT: A 438 PHE cc_start: 0.7998 (OUTLIER) cc_final: 0.7628 (t80) outliers start: 17 outliers final: 12 residues processed: 86 average time/residue: 0.0430 time to fit residues: 5.2443 Evaluate side-chains 86 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 HIS Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 502 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 35 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 22 optimal weight: 0.4980 chunk 8 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4017 r_free = 0.4017 target = 0.167162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.129122 restraints weight = 4643.113| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 2.71 r_work: 0.3470 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3471 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3471 r_free = 0.3471 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3471 r_free = 0.3471 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3471 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3809 Z= 0.140 Angle : 0.581 6.913 5194 Z= 0.279 Chirality : 0.038 0.127 614 Planarity : 0.005 0.056 651 Dihedral : 7.536 73.023 536 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 3.86 % Allowed : 16.97 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.72 (0.39), residues: 481 helix: 2.04 (0.27), residues: 362 sheet: -1.64 (1.60), residues: 10 loop : 1.59 (0.67), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 466 TYR 0.010 0.001 TYR A 169 PHE 0.017 0.001 PHE A 351 TRP 0.008 0.001 TRP A 274 HIS 0.005 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 3807) covalent geometry : angle 0.58063 ( 5190) SS BOND : bond 0.00326 ( 2) SS BOND : angle 0.42771 ( 4) hydrogen bonds : bond 0.03867 ( 258) hydrogen bonds : angle 3.80625 ( 768) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 962 Ramachandran restraints generated. 481 Oldfield, 0 Emsley, 481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 962 Ramachandran restraints generated. 481 Oldfield, 0 Emsley, 481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.138 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 GLN cc_start: 0.8919 (tm-30) cc_final: 0.8652 (tm-30) REVERT: A 206 CYS cc_start: 0.7211 (OUTLIER) cc_final: 0.6775 (t) REVERT: A 390 ASN cc_start: 0.7091 (m-40) cc_final: 0.6732 (m-40) REVERT: A 438 PHE cc_start: 0.7798 (OUTLIER) cc_final: 0.7456 (t80) outliers start: 15 outliers final: 12 residues processed: 83 average time/residue: 0.0377 time to fit residues: 4.5102 Evaluate side-chains 85 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 HIS Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 502 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 37 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 33 optimal weight: 0.3980 chunk 23 optimal weight: 0.4980 chunk 34 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4056 r_free = 0.4056 target = 0.171033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.131723 restraints weight = 4591.589| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 2.83 r_work: 0.3473 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3494 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3494 r_free = 0.3494 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3494 r_free = 0.3494 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3494 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3809 Z= 0.134 Angle : 0.583 9.281 5194 Z= 0.278 Chirality : 0.038 0.173 614 Planarity : 0.005 0.055 651 Dihedral : 6.775 60.716 536 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.60 % Allowed : 17.48 % Favored : 78.92 % 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 aren not related in a simple way. whole: 2.66 (0.39), residues: 481 helix: 2.02 (0.27), residues: 362 sheet: -1.55 (1.63), residues: 10 loop : 1.48 (0.66), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 310 TYR 0.018 0.001 TYR A 169 PHE 0.016 0.001 PHE A 351 TRP 0.007 0.001 TRP A 274 HIS 0.005 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 3807) covalent geometry : angle 0.58343 ( 5190) SS BOND : bond 0.00292 ( 2) SS BOND : angle 0.39931 ( 4) hydrogen bonds : bond 0.03794 ( 258) hydrogen bonds : angle 3.80611 ( 768) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 962 Ramachandran restraints generated. 481 Oldfield, 0 Emsley, 481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 962 Ramachandran restraints generated. 481 Oldfield, 0 Emsley, 481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.135 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 GLN cc_start: 0.8960 (tm-30) cc_final: 0.8726 (tm-30) REVERT: A 206 CYS cc_start: 0.7244 (OUTLIER) cc_final: 0.6829 (t) REVERT: A 358 MET cc_start: 0.6611 (mmm) cc_final: 0.6208 (mmm) REVERT: A 386 PHE cc_start: 0.7547 (t80) cc_final: 0.7009 (t80) REVERT: A 390 ASN cc_start: 0.7078 (m-40) cc_final: 0.6716 (m-40) REVERT: A 438 PHE cc_start: 0.7815 (OUTLIER) cc_final: 0.7470 (t80) outliers start: 14 outliers final: 12 residues processed: 82 average time/residue: 0.0424 time to fit residues: 4.9736 Evaluate side-chains 85 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 HIS Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 502 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 17 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.4021 r_free = 0.4021 target = 0.166716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.127740 restraints weight = 4583.567| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 2.78 r_work: 0.3452 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3465 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3465 r_free = 0.3465 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3465 r_free = 0.3465 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3465 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 3809 Z= 0.144 Angle : 0.593 8.601 5194 Z= 0.286 Chirality : 0.038 0.127 614 Planarity : 0.005 0.056 651 Dihedral : 5.367 49.049 536 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.86 % Allowed : 18.25 % Favored : 77.89 % 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 aren not related in a simple way. whole: 2.68 (0.39), residues: 481 helix: 2.01 (0.27), residues: 363 sheet: -1.51 (1.63), residues: 10 loop : 1.59 (0.66), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 466 TYR 0.009 0.001 TYR A 169 PHE 0.017 0.001 PHE A 351 TRP 0.007 0.001 TRP A 274 HIS 0.005 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 3807) covalent geometry : angle 0.59275 ( 5190) SS BOND : bond 0.00324 ( 2) SS BOND : angle 0.43629 ( 4) hydrogen bonds : bond 0.03881 ( 258) hydrogen bonds : angle 3.76943 ( 768) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 962 Ramachandran restraints generated. 481 Oldfield, 0 Emsley, 481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 962 Ramachandran restraints generated. 481 Oldfield, 0 Emsley, 481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 0.135 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 GLN cc_start: 0.8962 (tm-30) cc_final: 0.8735 (tm-30) REVERT: A 142 MET cc_start: 0.8281 (mmm) cc_final: 0.7456 (mmt) REVERT: A 206 CYS cc_start: 0.7312 (OUTLIER) cc_final: 0.6885 (t) REVERT: A 358 MET cc_start: 0.6867 (mmm) cc_final: 0.6399 (mmm) REVERT: A 386 PHE cc_start: 0.7611 (t80) cc_final: 0.7012 (t80) REVERT: A 390 ASN cc_start: 0.7108 (m-40) cc_final: 0.6575 (m-40) REVERT: A 438 PHE cc_start: 0.7900 (OUTLIER) cc_final: 0.7487 (t80) outliers start: 15 outliers final: 13 residues processed: 81 average time/residue: 0.0407 time to fit residues: 4.7180 Evaluate side-chains 84 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 HIS Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 502 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 16 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 18 optimal weight: 0.0270 chunk 22 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 27 optimal weight: 0.0010 chunk 19 optimal weight: 0.7980 chunk 2 optimal weight: 0.1980 chunk 41 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 38 optimal weight: 6.9990 overall best weight: 0.2844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.170608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.132336 restraints weight = 4502.999| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.76 r_work: 0.3505 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3527 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3527 r_free = 0.3527 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3527 r_free = 0.3527 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3527 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6898 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3809 Z= 0.119 Angle : 0.595 8.862 5194 Z= 0.282 Chirality : 0.037 0.144 614 Planarity : 0.005 0.056 651 Dihedral : 4.298 31.112 536 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.31 % Allowed : 21.08 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.80 (0.39), residues: 481 helix: 2.14 (0.28), residues: 357 sheet: -1.59 (1.55), residues: 10 loop : 1.50 (0.65), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 466 TYR 0.009 0.001 TYR A 354 PHE 0.016 0.001 PHE A 351 TRP 0.008 0.001 TRP A 247 HIS 0.005 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 3807) covalent geometry : angle 0.59489 ( 5190) SS BOND : bond 0.00201 ( 2) SS BOND : angle 0.29154 ( 4) hydrogen bonds : bond 0.03599 ( 258) hydrogen bonds : angle 3.70348 ( 768) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 962 Ramachandran restraints generated. 481 Oldfield, 0 Emsley, 481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 962 Ramachandran restraints generated. 481 Oldfield, 0 Emsley, 481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.167 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 GLN cc_start: 0.8948 (tm-30) cc_final: 0.8738 (tm-30) REVERT: A 206 CYS cc_start: 0.7199 (OUTLIER) cc_final: 0.6774 (t) REVERT: A 213 TRP cc_start: 0.7439 (m100) cc_final: 0.7144 (m100) REVERT: A 358 MET cc_start: 0.6460 (mmm) cc_final: 0.6159 (mmm) REVERT: A 386 PHE cc_start: 0.7427 (t80) cc_final: 0.6852 (t80) REVERT: A 390 ASN cc_start: 0.7046 (m-40) cc_final: 0.6521 (m-40) REVERT: A 438 PHE cc_start: 0.7758 (OUTLIER) cc_final: 0.7471 (t80) outliers start: 9 outliers final: 6 residues processed: 84 average time/residue: 0.0456 time to fit residues: 5.1615 Evaluate side-chains 81 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 HIS Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 475 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 21 optimal weight: 2.9990 chunk 46 optimal weight: 0.0980 chunk 19 optimal weight: 0.0970 chunk 34 optimal weight: 0.3980 chunk 18 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 4 optimal weight: 0.0030 chunk 44 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.2388 ------------------------------------------------------------------------------- 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 = 0.4064 r_free = 0.4064 target = 0.171613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.134802 restraints weight = 4434.985| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 2.69 r_work: 0.3522 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3549 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3549 r_free = 0.3549 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3549 r_free = 0.3549 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3549 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3809 Z= 0.116 Angle : 0.593 10.220 5194 Z= 0.280 Chirality : 0.037 0.129 614 Planarity : 0.005 0.056 651 Dihedral : 3.799 15.703 536 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.06 % Allowed : 21.85 % Favored : 76.09 % 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 aren not related in a simple way. whole: 2.84 (0.39), residues: 481 helix: 2.18 (0.27), residues: 357 sheet: -1.55 (1.50), residues: 10 loop : 1.48 (0.64), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 466 TYR 0.008 0.001 TYR A 444 PHE 0.017 0.001 PHE A 351 TRP 0.008 0.001 TRP A 247 HIS 0.005 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 3807) covalent geometry : angle 0.59348 ( 5190) SS BOND : bond 0.00178 ( 2) SS BOND : angle 0.28611 ( 4) hydrogen bonds : bond 0.03544 ( 258) hydrogen bonds : angle 3.64688 ( 768) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 998.47 seconds wall clock time: 17 minutes 52.45 seconds (1072.45 seconds total)