Starting phenix.real_space_refine on Fri Aug 22 13:00:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z7z_39833/08_2025/8z7z_39833.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z7z_39833/08_2025/8z7z_39833.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8z7z_39833/08_2025/8z7z_39833.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z7z_39833/08_2025/8z7z_39833.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8z7z_39833/08_2025/8z7z_39833.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z7z_39833/08_2025/8z7z_39833.map" } resolution = 3.23 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= 0.059 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 12 5.16 5 C 1886 2.51 5 N 436 2.21 5 O 500 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 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: 2834 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 2816 Classifications: {'peptide': 389} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 12, 'TRANS': 376} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 282 Unresolved non-hydrogen angles: 364 Unresolved non-hydrogen dihedrals: 259 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'PHE:plan': 6, 'TYR:plan': 6, 'ASP:plan': 2, 'GLN:plan1': 2, 'TRP:plan': 4, 'ASN:plan1': 2, 'ARG:plan': 4, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 162 Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'VIB': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.11, per 1000 atoms: 0.39 Number of scatterers: 2834 At special positions: 0 Unit cell: (78.288, 68.036, 66.172, 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 12 16.00 O 500 8.00 N 436 7.00 C 1886 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.31 Conformation dependent library (CDL) restraints added in 129.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 734 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 0 sheets defined 86.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 31 through 46 Processing helix chain 'A' and resid 53 through 58 Processing helix chain 'A' and resid 65 through 95 removed outlier: 5.443A pdb=" N TYR A 74 " --> pdb=" O PHE A 70 " (cutoff:3.500A) Proline residue: A 75 - end of helix removed outlier: 3.783A pdb=" N THR A 78 " --> pdb=" O TYR A 74 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N PHE A 86 " --> pdb=" O LEU A 82 " (cutoff:3.500A) Proline residue: A 87 - end of helix removed outlier: 3.666A pdb=" N ASP A 93 " --> pdb=" O PHE A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 117 removed outlier: 3.855A pdb=" N LEU A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 136 Processing helix chain 'A' and resid 137 through 145 removed outlier: 4.016A pdb=" N ILE A 145 " --> pdb=" O TYR A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 148 No H-bonds generated for 'chain 'A' and resid 146 through 148' Processing helix chain 'A' and resid 153 through 182 removed outlier: 3.664A pdb=" N VAL A 182 " --> pdb=" O ILE A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 206 Processing helix chain 'A' and resid 279 through 289 Processing helix chain 'A' and resid 292 through 297 removed outlier: 3.628A pdb=" N LEU A 296 " --> pdb=" O SER A 292 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N CYS A 297 " --> pdb=" O ARG A 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 292 through 297' Processing helix chain 'A' and resid 298 through 324 removed outlier: 4.177A pdb=" N ASN A 314 " --> pdb=" O PHE A 310 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N TYR A 315 " --> pdb=" O GLN A 311 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLN A 317 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLY A 318 " --> pdb=" O ASN A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 352 removed outlier: 4.104A pdb=" N VAL A 336 " --> pdb=" O TYR A 332 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR A 341 " --> pdb=" O GLU A 337 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLY A 352 " --> pdb=" O VAL A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 383 removed outlier: 3.963A pdb=" N TRP A 361 " --> pdb=" O SER A 357 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLU A 363 " --> pdb=" O SER A 359 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N MET A 364 " --> pdb=" O THR A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 415 Processing helix chain 'A' and resid 416 through 418 No H-bonds generated for 'chain 'A' and resid 416 through 418' Processing helix chain 'A' and resid 419 through 443 removed outlier: 3.715A pdb=" N THR A 428 " --> pdb=" O PHE A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 483 removed outlier: 3.592A pdb=" N PHE A 456 " --> pdb=" O ILE A 452 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LEU A 457 " --> pdb=" O THR A 453 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ARG A 483 " --> pdb=" O MET A 479 " (cutoff:3.500A) 237 hydrogen bonds defined for protein. 711 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: 0.34 Time building geometry restraints manager: 0.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 849 1.34 - 1.46: 583 1.46 - 1.57: 1452 1.57 - 1.69: 2 1.69 - 1.81: 16 Bond restraints: 2902 Sorted by residual: bond pdb=" C5 VIB A 501 " pdb=" S1 VIB A 501 " ideal model delta sigma weight residual 1.721 1.591 0.130 2.00e-02 2.50e+03 4.22e+01 bond pdb=" C4A VIB A 501 " pdb=" N4A VIB A 501 " ideal model delta sigma weight residual 1.347 1.453 -0.106 2.00e-02 2.50e+03 2.81e+01 bond pdb=" C4 VIB A 501 " pdb=" N3 VIB A 501 " ideal model delta sigma weight residual 1.385 1.476 -0.091 2.00e-02 2.50e+03 2.09e+01 bond pdb=" C2 VIB A 501 " pdb=" N3 VIB A 501 " ideal model delta sigma weight residual 1.315 1.395 -0.080 2.00e-02 2.50e+03 1.61e+01 bond pdb=" C4 VIB A 501 " pdb=" C5 VIB A 501 " ideal model delta sigma weight residual 1.358 1.416 -0.058 2.00e-02 2.50e+03 8.54e+00 ... (remaining 2897 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 3852 1.63 - 3.26: 108 3.26 - 4.88: 21 4.88 - 6.51: 11 6.51 - 8.14: 1 Bond angle restraints: 3993 Sorted by residual: angle pdb=" C CYS A 297 " pdb=" N TRP A 298 " pdb=" CA TRP A 298 " ideal model delta sigma weight residual 121.54 127.27 -5.73 1.91e+00 2.74e-01 9.01e+00 angle pdb=" C2 VIB A 501 " pdb=" S1 VIB A 501 " pdb=" C5 VIB A 501 " ideal model delta sigma weight residual 91.25 99.39 -8.14 3.00e+00 1.11e-01 7.36e+00 angle pdb=" C ASN A 71 " pdb=" N GLU A 72 " pdb=" CA GLU A 72 " ideal model delta sigma weight residual 121.54 116.45 5.09 1.91e+00 2.74e-01 7.10e+00 angle pdb=" C LEU A 53 " pdb=" N THR A 54 " pdb=" CA THR A 54 " ideal model delta sigma weight residual 120.09 123.37 -3.28 1.25e+00 6.40e-01 6.89e+00 angle pdb=" CA TYR A 390 " pdb=" CB TYR A 390 " pdb=" CG TYR A 390 " ideal model delta sigma weight residual 113.90 118.18 -4.28 1.80e+00 3.09e-01 5.66e+00 ... (remaining 3988 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.67: 1502 16.67 - 33.33: 112 33.33 - 50.00: 19 50.00 - 66.66: 4 66.66 - 83.33: 4 Dihedral angle restraints: 1641 sinusoidal: 498 harmonic: 1143 Sorted by residual: dihedral pdb=" CA ARG A 96 " pdb=" C ARG A 96 " pdb=" N TYR A 97 " pdb=" CA TYR A 97 " ideal model delta harmonic sigma weight residual 180.00 163.19 16.81 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CB GLU A 72 " pdb=" CG GLU A 72 " pdb=" CD GLU A 72 " pdb=" OE1 GLU A 72 " ideal model delta sinusoidal sigma weight residual 0.00 -83.33 83.33 1 3.00e+01 1.11e-03 9.43e+00 dihedral pdb=" CA LYS A 322 " pdb=" CB LYS A 322 " pdb=" CG LYS A 322 " pdb=" CD LYS A 322 " ideal model delta sinusoidal sigma weight residual -60.00 -110.45 50.45 3 1.50e+01 4.44e-03 8.90e+00 ... (remaining 1638 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 342 0.039 - 0.079: 122 0.079 - 0.118: 25 0.118 - 0.158: 5 0.158 - 0.197: 3 Chirality restraints: 497 Sorted by residual: chirality pdb=" CG LEU A 82 " pdb=" CB LEU A 82 " pdb=" CD1 LEU A 82 " pdb=" CD2 LEU A 82 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.71e-01 chirality pdb=" CB ILE A 331 " pdb=" CA ILE A 331 " pdb=" CG1 ILE A 331 " pdb=" CG2 ILE A 331 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.25e-01 chirality pdb=" CB ILE A 386 " pdb=" CA ILE A 386 " pdb=" CG1 ILE A 386 " pdb=" CG2 ILE A 386 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.49e-01 ... (remaining 494 not shown) Planarity restraints: 484 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 390 " -0.021 2.00e-02 2.50e+03 1.94e-02 7.52e+00 pdb=" CG TYR A 390 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR A 390 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR A 390 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR A 390 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 390 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 390 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 390 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 298 " 0.011 2.00e-02 2.50e+03 2.26e-02 5.10e+00 pdb=" C TRP A 298 " -0.039 2.00e-02 2.50e+03 pdb=" O TRP A 298 " 0.015 2.00e-02 2.50e+03 pdb=" N SER A 299 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 50 " -0.035 5.00e-02 4.00e+02 5.26e-02 4.43e+00 pdb=" N PRO A 51 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 51 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 51 " -0.029 5.00e-02 4.00e+02 ... (remaining 481 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 88 2.72 - 3.26: 3143 3.26 - 3.81: 4976 3.81 - 4.35: 5756 4.35 - 4.90: 9634 Nonbonded interactions: 23597 Sorted by model distance: nonbonded pdb=" O LEU A 304 " pdb=" OH TYR A 462 " model vdw 2.169 3.040 nonbonded pdb=" OG SER A 173 " pdb=" O GLY A 334 " model vdw 2.176 3.040 nonbonded pdb=" O VAL A 312 " pdb=" OG1 THR A 316 " model vdw 2.230 3.040 nonbonded pdb=" ND2 ASN A 71 " pdb=" O VAL A 443 " model vdw 2.307 3.120 nonbonded pdb=" OE2 GLU A 50 " pdb=" OH TYR A 131 " model vdw 2.311 3.040 ... (remaining 23592 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: 1.880 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 5.660 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 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: 8.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6386 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 0.130 2902 Z= 0.267 Angle : 0.710 8.140 3993 Z= 0.364 Chirality : 0.044 0.197 497 Planarity : 0.005 0.053 484 Dihedral : 13.231 83.330 907 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % 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 aren not related in a simple way. whole: 0.75 (0.43), residues: 385 helix: 1.00 (0.29), residues: 304 sheet: None (None), residues: 0 loop : -1.25 (0.75), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 67 TYR 0.048 0.002 TYR A 390 PHE 0.027 0.002 PHE A 396 TRP 0.028 0.002 TRP A 301 Details of bonding type rmsd covalent geometry : bond 0.00547 ( 2902) covalent geometry : angle 0.71012 ( 3993) hydrogen bonds : bond 0.11548 ( 237) hydrogen bonds : angle 5.21634 ( 711) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.103 Fit side-chains REVERT: A 96 ARG cc_start: 0.4145 (mmt180) cc_final: 0.3932 (mmt180) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.0496 time to fit residues: 5.8862 Evaluate side-chains 74 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 24 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.0470 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 0.0370 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 overall best weight: 0.4556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 GLN A 435 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4757 r_free = 0.4757 target = 0.238733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.218820 restraints weight = 3678.601| |-----------------------------------------------------------------------------| r_work (start): 0.4596 rms_B_bonded: 2.01 r_work: 0.4475 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.4475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6660 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2902 Z= 0.130 Angle : 0.569 5.542 3993 Z= 0.305 Chirality : 0.039 0.120 497 Planarity : 0.005 0.049 484 Dihedral : 5.632 73.195 418 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.91 % Allowed : 12.60 % Favored : 85.50 % 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: 1.12 (0.42), residues: 385 helix: 1.31 (0.29), residues: 305 sheet: None (None), residues: 0 loop : -1.38 (0.70), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 162 TYR 0.049 0.002 TYR A 390 PHE 0.021 0.002 PHE A 396 TRP 0.014 0.002 TRP A 112 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 2902) covalent geometry : angle 0.56893 ( 3993) hydrogen bonds : bond 0.03305 ( 237) hydrogen bonds : angle 4.15913 ( 711) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 77 time to evaluate : 0.087 Fit side-chains REVERT: A 96 ARG cc_start: 0.3828 (mmt180) cc_final: 0.3530 (mmt180) REVERT: A 108 LEU cc_start: 0.7355 (mt) cc_final: 0.6869 (mt) REVERT: A 138 GLU cc_start: 0.6010 (mm-30) cc_final: 0.5370 (mm-30) outliers start: 5 outliers final: 1 residues processed: 79 average time/residue: 0.0628 time to fit residues: 6.0122 Evaluate side-chains 79 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 78 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 0 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 25 optimal weight: 0.0980 chunk 28 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 4 optimal weight: 0.2980 chunk 10 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 = 0.4758 r_free = 0.4758 target = 0.238715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.219816 restraints weight = 3732.215| |-----------------------------------------------------------------------------| r_work (start): 0.4602 rms_B_bonded: 1.86 r_work: 0.4495 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work (final): 0.4495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6659 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2902 Z= 0.126 Angle : 0.548 5.106 3993 Z= 0.295 Chirality : 0.038 0.114 497 Planarity : 0.005 0.050 484 Dihedral : 5.418 69.100 418 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.29 % Allowed : 18.32 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.42 (0.42), residues: 385 helix: 1.56 (0.29), residues: 306 sheet: None (None), residues: 0 loop : -1.46 (0.69), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 96 TYR 0.041 0.002 TYR A 390 PHE 0.023 0.002 PHE A 89 TRP 0.014 0.002 TRP A 112 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 2902) covalent geometry : angle 0.54753 ( 3993) hydrogen bonds : bond 0.03199 ( 237) hydrogen bonds : angle 4.05895 ( 711) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.117 Fit side-chains REVERT: A 96 ARG cc_start: 0.3984 (mmt180) cc_final: 0.3656 (mmt180) REVERT: A 108 LEU cc_start: 0.7331 (mt) cc_final: 0.6836 (mt) REVERT: A 317 GLN cc_start: 0.7366 (mm-40) cc_final: 0.7113 (mt0) REVERT: A 392 SER cc_start: 0.7188 (p) cc_final: 0.6650 (t) outliers start: 6 outliers final: 1 residues processed: 84 average time/residue: 0.0586 time to fit residues: 6.0687 Evaluate side-chains 79 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 78 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 370 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 29 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 6 optimal weight: 0.0170 chunk 5 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4729 r_free = 0.4729 target = 0.235258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.216169 restraints weight = 3714.548| |-----------------------------------------------------------------------------| r_work (start): 0.4573 rms_B_bonded: 1.84 r_work: 0.4465 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work (final): 0.4465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6720 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2902 Z= 0.141 Angle : 0.564 5.161 3993 Z= 0.303 Chirality : 0.040 0.150 497 Planarity : 0.005 0.050 484 Dihedral : 5.322 65.478 418 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.67 % Allowed : 19.85 % Favored : 77.48 % 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: 1.46 (0.43), residues: 385 helix: 1.55 (0.29), residues: 309 sheet: None (None), residues: 0 loop : -1.36 (0.72), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 67 TYR 0.048 0.002 TYR A 390 PHE 0.021 0.002 PHE A 89 TRP 0.015 0.001 TRP A 112 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 2902) covalent geometry : angle 0.56422 ( 3993) hydrogen bonds : bond 0.03279 ( 237) hydrogen bonds : angle 4.09544 ( 711) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 0.101 Fit side-chains REVERT: A 96 ARG cc_start: 0.4016 (mmt180) cc_final: 0.3686 (mmt180) REVERT: A 108 LEU cc_start: 0.7390 (mt) cc_final: 0.6890 (mt) REVERT: A 435 GLN cc_start: 0.5913 (OUTLIER) cc_final: 0.5688 (tt0) outliers start: 7 outliers final: 5 residues processed: 81 average time/residue: 0.0603 time to fit residues: 5.9843 Evaluate side-chains 78 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 435 GLN Chi-restraints excluded: chain A residue 442 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 15 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 26 optimal weight: 10.0000 chunk 33 optimal weight: 0.5980 chunk 5 optimal weight: 0.2980 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 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 = 0.4740 r_free = 0.4740 target = 0.236611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.217454 restraints weight = 3616.229| |-----------------------------------------------------------------------------| r_work (start): 0.4581 rms_B_bonded: 1.92 r_work: 0.4466 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.4466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6748 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2902 Z= 0.142 Angle : 0.558 5.160 3993 Z= 0.299 Chirality : 0.039 0.158 497 Planarity : 0.005 0.053 484 Dihedral : 5.251 63.553 418 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.44 % Allowed : 20.61 % Favored : 75.95 % 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: 1.57 (0.43), residues: 385 helix: 1.65 (0.29), residues: 307 sheet: None (None), residues: 0 loop : -1.39 (0.71), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 397 TYR 0.037 0.002 TYR A 390 PHE 0.018 0.002 PHE A 89 TRP 0.015 0.002 TRP A 112 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 2902) covalent geometry : angle 0.55766 ( 3993) hydrogen bonds : bond 0.03296 ( 237) hydrogen bonds : angle 4.02957 ( 711) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.107 Fit side-chains REVERT: A 96 ARG cc_start: 0.4094 (mmt180) cc_final: 0.3777 (mmt180) REVERT: A 108 LEU cc_start: 0.7436 (mt) cc_final: 0.7206 (tp) outliers start: 9 outliers final: 7 residues processed: 81 average time/residue: 0.0577 time to fit residues: 5.7674 Evaluate side-chains 82 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 442 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 8 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 26 optimal weight: 0.1980 chunk 28 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 36 optimal weight: 0.3980 chunk 30 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4747 r_free = 0.4747 target = 0.237205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.218861 restraints weight = 3714.711| |-----------------------------------------------------------------------------| r_work (start): 0.4623 rms_B_bonded: 1.77 r_work: 0.4509 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work (final): 0.4509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6738 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2902 Z= 0.136 Angle : 0.572 7.370 3993 Z= 0.300 Chirality : 0.039 0.156 497 Planarity : 0.005 0.053 484 Dihedral : 5.189 62.455 418 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 4.20 % Allowed : 22.52 % Favored : 73.28 % 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: 1.53 (0.42), residues: 385 helix: 1.60 (0.29), residues: 307 sheet: None (None), residues: 0 loop : -1.32 (0.71), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 96 TYR 0.032 0.002 TYR A 390 PHE 0.024 0.002 PHE A 89 TRP 0.015 0.002 TRP A 112 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 2902) covalent geometry : angle 0.57201 ( 3993) hydrogen bonds : bond 0.03243 ( 237) hydrogen bonds : angle 4.02277 ( 711) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.098 Fit side-chains REVERT: A 96 ARG cc_start: 0.4150 (mmt180) cc_final: 0.3826 (mmt180) REVERT: A 108 LEU cc_start: 0.7423 (mt) cc_final: 0.6878 (mt) REVERT: A 337 GLU cc_start: 0.6258 (mm-30) cc_final: 0.5923 (mm-30) outliers start: 11 outliers final: 8 residues processed: 80 average time/residue: 0.0588 time to fit residues: 5.7569 Evaluate side-chains 82 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ARG Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 443 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 8 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 35 optimal weight: 0.0170 chunk 14 optimal weight: 0.4980 chunk 11 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 overall best weight: 0.5218 ------------------------------------------------------------------------------- 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 = 0.4745 r_free = 0.4745 target = 0.236908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.217462 restraints weight = 3717.146| |-----------------------------------------------------------------------------| r_work (start): 0.4599 rms_B_bonded: 1.96 r_work: 0.4488 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.4488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6736 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2902 Z= 0.135 Angle : 0.569 6.400 3993 Z= 0.300 Chirality : 0.039 0.164 497 Planarity : 0.005 0.055 484 Dihedral : 5.156 62.295 418 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.67 % Allowed : 23.66 % Favored : 73.66 % 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: 1.64 (0.43), residues: 385 helix: 1.68 (0.29), residues: 307 sheet: None (None), residues: 0 loop : -1.27 (0.72), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 397 TYR 0.035 0.002 TYR A 400 PHE 0.025 0.002 PHE A 89 TRP 0.015 0.001 TRP A 112 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 2902) covalent geometry : angle 0.56896 ( 3993) hydrogen bonds : bond 0.03226 ( 237) hydrogen bonds : angle 4.03018 ( 711) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.103 Fit side-chains REVERT: A 96 ARG cc_start: 0.4097 (mmt180) cc_final: 0.3775 (mmt180) REVERT: A 108 LEU cc_start: 0.7388 (mt) cc_final: 0.6848 (mt) outliers start: 7 outliers final: 7 residues processed: 74 average time/residue: 0.0559 time to fit residues: 5.1651 Evaluate side-chains 80 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ARG Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 370 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 4 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 5 optimal weight: 0.4980 chunk 26 optimal weight: 8.9990 chunk 10 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 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 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4734 r_free = 0.4734 target = 0.235550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.215929 restraints weight = 3748.084| |-----------------------------------------------------------------------------| r_work (start): 0.4570 rms_B_bonded: 1.97 r_work: 0.4457 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.4457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6771 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2902 Z= 0.151 Angle : 0.600 7.240 3993 Z= 0.317 Chirality : 0.040 0.166 497 Planarity : 0.005 0.057 484 Dihedral : 5.169 61.850 418 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.20 % Allowed : 23.66 % Favored : 72.14 % 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: 1.62 (0.42), residues: 385 helix: 1.66 (0.29), residues: 305 sheet: None (None), residues: 0 loop : -1.20 (0.72), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 397 TYR 0.028 0.002 TYR A 390 PHE 0.026 0.002 PHE A 89 TRP 0.015 0.002 TRP A 298 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 2902) covalent geometry : angle 0.59961 ( 3993) hydrogen bonds : bond 0.03295 ( 237) hydrogen bonds : angle 4.08289 ( 711) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.100 Fit side-chains REVERT: A 96 ARG cc_start: 0.4067 (mmt180) cc_final: 0.3794 (mmt180) REVERT: A 108 LEU cc_start: 0.7439 (mt) cc_final: 0.6891 (mt) outliers start: 11 outliers final: 6 residues processed: 76 average time/residue: 0.0580 time to fit residues: 5.4329 Evaluate side-chains 78 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 442 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 23 optimal weight: 0.0000 chunk 5 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 33 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 435 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4746 r_free = 0.4746 target = 0.236847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.217270 restraints weight = 3730.702| |-----------------------------------------------------------------------------| r_work (start): 0.4582 rms_B_bonded: 1.96 r_work: 0.4467 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.4467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6749 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2902 Z= 0.142 Angle : 0.579 5.206 3993 Z= 0.308 Chirality : 0.040 0.167 497 Planarity : 0.005 0.055 484 Dihedral : 5.178 61.594 418 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.67 % Allowed : 23.66 % Favored : 73.66 % 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: 1.62 (0.43), residues: 385 helix: 1.64 (0.29), residues: 305 sheet: None (None), residues: 0 loop : -1.07 (0.76), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 67 TYR 0.026 0.002 TYR A 390 PHE 0.026 0.002 PHE A 89 TRP 0.020 0.002 TRP A 112 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 2902) covalent geometry : angle 0.57874 ( 3993) hydrogen bonds : bond 0.03256 ( 237) hydrogen bonds : angle 4.09508 ( 711) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.121 Fit side-chains REVERT: A 96 ARG cc_start: 0.4038 (mmt180) cc_final: 0.3782 (mmt180) REVERT: A 108 LEU cc_start: 0.7386 (mt) cc_final: 0.6921 (mt) outliers start: 7 outliers final: 5 residues processed: 74 average time/residue: 0.0517 time to fit residues: 4.7910 Evaluate side-chains 74 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 442 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 37 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 21 optimal weight: 0.4980 chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 3 optimal weight: 0.3980 chunk 30 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 0.0980 chunk 16 optimal weight: 1.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 GLN ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4755 r_free = 0.4755 target = 0.237824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.218444 restraints weight = 3717.534| |-----------------------------------------------------------------------------| r_work (start): 0.4591 rms_B_bonded: 1.95 r_work: 0.4478 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.4478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6734 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2902 Z= 0.139 Angle : 0.615 8.568 3993 Z= 0.320 Chirality : 0.039 0.165 497 Planarity : 0.005 0.055 484 Dihedral : 5.290 61.653 418 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.29 % Allowed : 24.81 % Favored : 72.90 % 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: 1.59 (0.43), residues: 385 helix: 1.59 (0.29), residues: 307 sheet: None (None), residues: 0 loop : -1.03 (0.75), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 67 TYR 0.025 0.002 TYR A 390 PHE 0.027 0.002 PHE A 89 TRP 0.037 0.002 TRP A 112 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 2902) covalent geometry : angle 0.61475 ( 3993) hydrogen bonds : bond 0.03264 ( 237) hydrogen bonds : angle 4.09660 ( 711) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.114 Fit side-chains REVERT: A 96 ARG cc_start: 0.3998 (mmt180) cc_final: 0.3733 (mmt180) REVERT: A 108 LEU cc_start: 0.7416 (mt) cc_final: 0.6899 (mt) outliers start: 6 outliers final: 6 residues processed: 71 average time/residue: 0.0547 time to fit residues: 4.8541 Evaluate side-chains 74 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 317 GLN Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 442 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 22 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 14 optimal weight: 0.0670 chunk 17 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 GLN ** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4737 r_free = 0.4737 target = 0.235709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.215970 restraints weight = 3695.962| |-----------------------------------------------------------------------------| r_work (start): 0.4571 rms_B_bonded: 1.95 r_work: 0.4453 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.4453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6765 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2902 Z= 0.152 Angle : 0.625 7.941 3993 Z= 0.328 Chirality : 0.040 0.163 497 Planarity : 0.005 0.056 484 Dihedral : 5.320 61.421 418 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.29 % Allowed : 25.19 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.57 (0.43), residues: 385 helix: 1.59 (0.29), residues: 307 sheet: None (None), residues: 0 loop : -1.09 (0.75), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 162 TYR 0.026 0.002 TYR A 390 PHE 0.028 0.002 PHE A 89 TRP 0.046 0.002 TRP A 112 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 2902) covalent geometry : angle 0.62491 ( 3993) hydrogen bonds : bond 0.03317 ( 237) hydrogen bonds : angle 4.13105 ( 711) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 868.88 seconds wall clock time: 15 minutes 43.35 seconds (943.35 seconds total)