Starting phenix.real_space_refine on Wed Mar 5 20:49:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y65_38966/03_2025/8y65_38966.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y65_38966/03_2025/8y65_38966.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y65_38966/03_2025/8y65_38966.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y65_38966/03_2025/8y65_38966.map" model { file = "/net/cci-nas-00/data/ceres_data/8y65_38966/03_2025/8y65_38966.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y65_38966/03_2025/8y65_38966.cif" } resolution = 3.51 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.171 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 13 5.16 5 C 2355 2.51 5 N 574 2.21 5 O 623 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3565 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3553 Classifications: {'peptide': 467} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 24, 'TRANS': 442} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'URC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.81, per 1000 atoms: 0.79 Number of scatterers: 3565 At special positions: 0 Unit cell: (84.5383, 62.5803, 69.1677, 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 13 16.00 O 623 8.00 N 574 7.00 C 2355 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: 1.00 Conformation dependent library (CDL) restraints added in 472.3 milliseconds 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 848 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 0 sheets defined 86.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 54 through 76 removed outlier: 4.372A pdb=" N PHE A 69 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LEU A 70 " --> pdb=" O GLY A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 98 Processing helix chain 'A' and resid 102 through 132 removed outlier: 4.794A pdb=" N PHE A 117 " --> pdb=" O THR A 113 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ALA A 118 " --> pdb=" O VAL A 114 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE A 119 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS A 129 " --> pdb=" O THR A 125 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N MET A 130 " --> pdb=" O LEU A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 157 Processing helix chain 'A' and resid 157 through 162 removed outlier: 4.116A pdb=" N ALA A 161 " --> pdb=" O CYS A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 193 removed outlier: 3.742A pdb=" N LEU A 167 " --> pdb=" O ALA A 163 " (cutoff:3.500A) Proline residue: A 186 - end of helix removed outlier: 3.848A pdb=" N GLU A 191 " --> pdb=" O MET A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 196 No H-bonds generated for 'chain 'A' and resid 194 through 196' Processing helix chain 'A' and resid 197 through 219 removed outlier: 3.625A pdb=" N LEU A 201 " --> pdb=" O ILE A 197 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR A 205 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ALA A 206 " --> pdb=" O GLY A 202 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE A 209 " --> pdb=" O THR A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 237 removed outlier: 4.096A pdb=" N VAL A 237 " --> pdb=" O LEU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 249 removed outlier: 3.589A pdb=" N ALA A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 252 No H-bonds generated for 'chain 'A' and resid 250 through 252' Processing helix chain 'A' and resid 255 through 262 removed outlier: 3.799A pdb=" N LEU A 259 " --> pdb=" O SER A 255 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU A 262 " --> pdb=" O TYR A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 282 through 299 removed outlier: 3.501A pdb=" N ILE A 299 " --> pdb=" O VAL A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 310 Processing helix chain 'A' and resid 313 through 331 removed outlier: 4.333A pdb=" N GLY A 331 " --> pdb=" O TYR A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 338 Processing helix chain 'A' and resid 338 through 345 Processing helix chain 'A' and resid 352 through 379 removed outlier: 4.064A pdb=" N LEU A 373 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N GLU A 376 " --> pdb=" O GLY A 372 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N HIS A 377 " --> pdb=" O LEU A 373 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLY A 379 " --> pdb=" O ILE A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 404 Processing helix chain 'A' and resid 410 through 412 No H-bonds generated for 'chain 'A' and resid 410 through 412' Processing helix chain 'A' and resid 413 through 428 removed outlier: 4.043A pdb=" N VAL A 417 " --> pdb=" O TYR A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 442 removed outlier: 4.708A pdb=" N GLY A 439 " --> pdb=" O PHE A 435 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE A 442 " --> pdb=" O THR A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 476 Proline residue: A 470 - end of helix Processing helix chain 'A' and resid 481 through 499 Processing helix chain 'A' and resid 506 through 518 271 hydrogen bonds defined for protein. 801 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: 0.96 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1101 1.34 - 1.46: 872 1.46 - 1.58: 1664 1.58 - 1.70: 0 1.70 - 1.82: 18 Bond restraints: 3655 Sorted by residual: bond pdb=" C4 URC A 601 " pdb=" C5 URC A 601 " ideal model delta sigma weight residual 1.358 1.470 -0.112 2.00e-02 2.50e+03 3.15e+01 bond pdb=" C6 URC A 601 " pdb=" N1 URC A 601 " ideal model delta sigma weight residual 1.398 1.317 0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" C8 URC A 601 " pdb=" N9 URC A 601 " ideal model delta sigma weight residual 1.396 1.316 0.080 2.00e-02 2.50e+03 1.62e+01 bond pdb=" N ILE A 335 " pdb=" CA ILE A 335 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.25e-02 6.40e+03 1.10e+01 bond pdb=" C2 URC A 601 " pdb=" N3 URC A 601 " ideal model delta sigma weight residual 1.376 1.311 0.065 2.00e-02 2.50e+03 1.06e+01 ... (remaining 3650 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.81: 4930 2.81 - 5.62: 44 5.62 - 8.42: 11 8.42 - 11.23: 3 11.23 - 14.04: 1 Bond angle restraints: 4989 Sorted by residual: angle pdb=" N7 URC A 601 " pdb=" C8 URC A 601 " pdb=" N9 URC A 601 " ideal model delta sigma weight residual 104.73 118.77 -14.04 3.00e+00 1.11e-01 2.19e+01 angle pdb=" N ILE A 436 " pdb=" CA ILE A 436 " pdb=" C ILE A 436 " ideal model delta sigma weight residual 112.96 108.33 4.63 1.00e+00 1.00e+00 2.15e+01 angle pdb=" CA ILE A 335 " pdb=" C ILE A 335 " pdb=" N TRP A 336 " ideal model delta sigma weight residual 118.13 123.44 -5.31 1.37e+00 5.33e-01 1.50e+01 angle pdb=" N1 URC A 601 " pdb=" C2 URC A 601 " pdb=" N3 URC A 601 " ideal model delta sigma weight residual 114.62 124.69 -10.07 3.00e+00 1.11e-01 1.13e+01 angle pdb=" N ILE A 335 " pdb=" CA ILE A 335 " pdb=" C ILE A 335 " ideal model delta sigma weight residual 113.00 108.67 4.33 1.30e+00 5.92e-01 1.11e+01 ... (remaining 4984 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.37: 1911 17.37 - 34.73: 166 34.73 - 52.10: 26 52.10 - 69.46: 4 69.46 - 86.83: 4 Dihedral angle restraints: 2111 sinusoidal: 781 harmonic: 1330 Sorted by residual: dihedral pdb=" CA GLY A 331 " pdb=" C GLY A 331 " pdb=" N LEU A 332 " pdb=" CA LEU A 332 " ideal model delta harmonic sigma weight residual 180.00 163.26 16.74 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CB GLU A 223 " pdb=" CG GLU A 223 " pdb=" CD GLU A 223 " pdb=" OE1 GLU A 223 " ideal model delta sinusoidal sigma weight residual 0.00 -86.83 86.83 1 3.00e+01 1.11e-03 1.01e+01 dihedral pdb=" CB GLU A 287 " pdb=" CG GLU A 287 " pdb=" CD GLU A 287 " pdb=" OE1 GLU A 287 " ideal model delta sinusoidal sigma weight residual 0.00 86.24 -86.24 1 3.00e+01 1.11e-03 9.97e+00 ... (remaining 2108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 425 0.039 - 0.079: 125 0.079 - 0.118: 37 0.118 - 0.158: 3 0.158 - 0.197: 2 Chirality restraints: 592 Sorted by residual: chirality pdb=" CB ILE A 335 " pdb=" CA ILE A 335 " pdb=" CG1 ILE A 335 " pdb=" CG2 ILE A 335 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.70e-01 chirality pdb=" CB ILE A 197 " pdb=" CA ILE A 197 " pdb=" CG1 ILE A 197 " pdb=" CG2 ILE A 197 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.19 2.00e-01 2.50e+01 9.33e-01 chirality pdb=" CA ILE A 348 " pdb=" N ILE A 348 " pdb=" C ILE A 348 " pdb=" CB ILE A 348 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.52e-01 ... (remaining 589 not shown) Planarity restraints: 618 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 381 " -0.042 5.00e-02 4.00e+02 6.31e-02 6.37e+00 pdb=" N PRO A 382 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 382 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 382 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 255 " 0.038 5.00e-02 4.00e+02 5.83e-02 5.44e+00 pdb=" N PRO A 256 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 256 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 256 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 335 " 0.012 2.00e-02 2.50e+03 2.31e-02 5.32e+00 pdb=" C ILE A 335 " -0.040 2.00e-02 2.50e+03 pdb=" O ILE A 335 " 0.014 2.00e-02 2.50e+03 pdb=" N TRP A 336 " 0.014 2.00e-02 2.50e+03 ... (remaining 615 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 673 2.76 - 3.30: 3548 3.30 - 3.83: 6129 3.83 - 4.37: 6408 4.37 - 4.90: 11451 Nonbonded interactions: 28209 Sorted by model distance: nonbonded pdb=" NH2 ARG A 96 " pdb=" O GLY A 162 " model vdw 2.231 3.120 nonbonded pdb=" NE2 GLN A 328 " pdb=" OD1 ASN A 458 " model vdw 2.281 3.120 nonbonded pdb=" OE1 GLN A 328 " pdb=" ND2 ASN A 333 " model vdw 2.335 3.120 nonbonded pdb=" NZ LYS A 195 " pdb=" OE2 GLU A 288 " model vdw 2.343 3.120 nonbonded pdb=" O GLY A 136 " pdb=" OG1 THR A 140 " model vdw 2.353 3.040 ... (remaining 28204 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.490 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.810 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5316 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 3655 Z= 0.275 Angle : 0.734 14.038 4989 Z= 0.355 Chirality : 0.041 0.197 592 Planarity : 0.005 0.063 618 Dihedral : 13.646 86.828 1263 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.27 % Allowed : 0.27 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.42), residues: 465 helix: 1.61 (0.29), residues: 363 sheet: None (None), residues: 0 loop : -0.14 (0.69), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 93 HIS 0.002 0.000 HIS A 377 PHE 0.012 0.001 PHE A 208 TYR 0.007 0.001 TYR A 327 ARG 0.003 0.000 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 28 time to evaluate : 0.364 Fit side-chains REVERT: A 400 ILE cc_start: 0.7317 (tp) cc_final: 0.6686 (tt) outliers start: 1 outliers final: 1 residues processed: 29 average time/residue: 0.1496 time to fit residues: 5.7887 Evaluate side-chains 23 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 38 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 23 optimal weight: 9.9990 chunk 18 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 21 optimal weight: 7.9990 chunk 26 optimal weight: 0.0370 chunk 41 optimal weight: 0.5980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4836 r_free = 0.4836 target = 0.276821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.253866 restraints weight = 3972.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4689 r_free = 0.4689 target = 0.258120 restraints weight = 2391.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4711 r_free = 0.4711 target = 0.261121 restraints weight = 1616.414| |-----------------------------------------------------------------------------| r_work (final): 0.4686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5439 moved from start: 0.0863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3655 Z= 0.184 Angle : 0.590 7.530 4989 Z= 0.292 Chirality : 0.041 0.135 592 Planarity : 0.005 0.045 618 Dihedral : 4.139 20.969 500 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.27 % Allowed : 4.26 % Favored : 95.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.41), residues: 465 helix: 1.64 (0.28), residues: 364 sheet: None (None), residues: 0 loop : -0.29 (0.69), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 336 HIS 0.002 0.000 HIS A 377 PHE 0.017 0.001 PHE A 276 TYR 0.005 0.001 TYR A 233 ARG 0.006 0.000 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 25 time to evaluate : 0.373 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 26 average time/residue: 0.1081 time to fit residues: 4.2241 Evaluate side-chains 24 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 23 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 8 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 22 optimal weight: 0.0980 chunk 43 optimal weight: 0.9990 chunk 39 optimal weight: 0.2980 chunk 24 optimal weight: 7.9990 chunk 31 optimal weight: 0.5980 chunk 3 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 74 ASN ** A 144 ASN ** 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 = 0.4830 r_free = 0.4830 target = 0.277004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.254148 restraints weight = 3981.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4687 r_free = 0.4687 target = 0.258248 restraints weight = 2381.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.261172 restraints weight = 1622.719| |-----------------------------------------------------------------------------| r_work (final): 0.4728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5451 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3655 Z= 0.168 Angle : 0.565 6.480 4989 Z= 0.278 Chirality : 0.040 0.143 592 Planarity : 0.004 0.036 618 Dihedral : 3.968 16.551 498 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.80 % Allowed : 7.71 % Favored : 91.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.41), residues: 465 helix: 1.72 (0.28), residues: 362 sheet: None (None), residues: 0 loop : -0.39 (0.67), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 231 HIS 0.002 0.001 HIS A 377 PHE 0.013 0.001 PHE A 276 TYR 0.006 0.001 TYR A 258 ARG 0.004 0.000 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.421 Fit side-chains REVERT: A 324 MET cc_start: 0.7187 (mmm) cc_final: 0.6914 (mmm) outliers start: 3 outliers final: 2 residues processed: 25 average time/residue: 0.0787 time to fit residues: 3.2365 Evaluate side-chains 25 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 401 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 29 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.4790 r_free = 0.4790 target = 0.271705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.247980 restraints weight = 4022.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.252153 restraints weight = 2442.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4662 r_free = 0.4662 target = 0.254893 restraints weight = 1678.295| |-----------------------------------------------------------------------------| r_work (final): 0.4684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5585 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 3655 Z= 0.231 Angle : 0.610 5.605 4989 Z= 0.306 Chirality : 0.042 0.134 592 Planarity : 0.004 0.030 618 Dihedral : 4.148 15.827 498 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.06 % Allowed : 12.50 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.40), residues: 465 helix: 1.49 (0.28), residues: 367 sheet: None (None), residues: 0 loop : -0.90 (0.65), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 315 HIS 0.003 0.001 HIS A 377 PHE 0.007 0.001 PHE A 276 TYR 0.009 0.001 TYR A 233 ARG 0.003 0.000 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.337 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 25 average time/residue: 0.0817 time to fit residues: 3.4583 Evaluate side-chains 24 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 401 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 29 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 38 optimal weight: 0.0870 chunk 21 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 4 optimal weight: 0.0870 chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.6336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 ASN ** 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 = 0.4799 r_free = 0.4799 target = 0.273293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.249658 restraints weight = 4024.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.253856 restraints weight = 2419.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.256864 restraints weight = 1657.392| |-----------------------------------------------------------------------------| r_work (final): 0.4614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5511 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3655 Z= 0.183 Angle : 0.564 6.088 4989 Z= 0.282 Chirality : 0.041 0.179 592 Planarity : 0.004 0.032 618 Dihedral : 4.073 15.349 498 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.13 % Allowed : 13.56 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.40), residues: 465 helix: 1.55 (0.28), residues: 366 sheet: None (None), residues: 0 loop : -0.91 (0.64), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 231 HIS 0.002 0.001 HIS A 377 PHE 0.009 0.001 PHE A 69 TYR 0.007 0.001 TYR A 258 ARG 0.002 0.000 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 21 time to evaluate : 0.341 Fit side-chains REVERT: A 262 GLU cc_start: -0.0405 (OUTLIER) cc_final: -0.1245 (tp30) outliers start: 8 outliers final: 3 residues processed: 27 average time/residue: 0.0844 time to fit residues: 3.6644 Evaluate side-chains 25 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 401 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 31 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 25 optimal weight: 0.4980 chunk 21 optimal weight: 0.8980 chunk 17 optimal weight: 0.0010 chunk 6 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 3 optimal weight: 0.8980 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 ASN ** 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 = 0.4797 r_free = 0.4797 target = 0.272983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.248804 restraints weight = 4141.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.253125 restraints weight = 2507.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4668 r_free = 0.4668 target = 0.256116 restraints weight = 1726.438| |-----------------------------------------------------------------------------| r_work (final): 0.4603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5528 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3655 Z= 0.189 Angle : 0.577 8.467 4989 Z= 0.286 Chirality : 0.041 0.169 592 Planarity : 0.004 0.032 618 Dihedral : 4.058 15.136 498 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.60 % Allowed : 14.36 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.40), residues: 465 helix: 1.56 (0.28), residues: 366 sheet: None (None), residues: 0 loop : -1.02 (0.64), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 231 HIS 0.002 0.001 HIS A 377 PHE 0.009 0.001 PHE A 69 TYR 0.007 0.001 TYR A 258 ARG 0.002 0.000 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 24 time to evaluate : 0.321 Fit side-chains REVERT: A 262 GLU cc_start: -0.0387 (OUTLIER) cc_final: -0.1253 (tp30) REVERT: A 324 MET cc_start: 0.7291 (mmm) cc_final: 0.7081 (mmm) outliers start: 6 outliers final: 2 residues processed: 28 average time/residue: 0.0838 time to fit residues: 3.7169 Evaluate side-chains 26 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 401 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 32 optimal weight: 0.0980 chunk 21 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 44 optimal weight: 0.0770 chunk 1 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 ASN ** 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 = 0.4796 r_free = 0.4796 target = 0.273597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.250298 restraints weight = 4035.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.254471 restraints weight = 2469.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.256949 restraints weight = 1706.157| |-----------------------------------------------------------------------------| r_work (final): 0.4665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5542 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3655 Z= 0.169 Angle : 0.563 6.608 4989 Z= 0.278 Chirality : 0.041 0.181 592 Planarity : 0.004 0.033 618 Dihedral : 4.034 14.941 498 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.60 % Allowed : 14.63 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.40), residues: 465 helix: 1.55 (0.28), residues: 369 sheet: None (None), residues: 0 loop : -1.02 (0.65), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 231 HIS 0.002 0.001 HIS A 377 PHE 0.013 0.001 PHE A 276 TYR 0.007 0.001 TYR A 258 ARG 0.002 0.000 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 23 time to evaluate : 0.370 Fit side-chains REVERT: A 262 GLU cc_start: -0.0393 (OUTLIER) cc_final: -0.1269 (tp30) REVERT: A 324 MET cc_start: 0.7262 (mmm) cc_final: 0.7051 (mmm) outliers start: 6 outliers final: 5 residues processed: 26 average time/residue: 0.0990 time to fit residues: 4.0284 Evaluate side-chains 29 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 23 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 480 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 41 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 27 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 38 optimal weight: 0.0670 chunk 31 optimal weight: 0.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 ASN ** 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 = 0.4785 r_free = 0.4785 target = 0.271944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.248538 restraints weight = 4030.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.252639 restraints weight = 2459.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.255461 restraints weight = 1698.868| |-----------------------------------------------------------------------------| r_work (final): 0.4638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5568 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3655 Z= 0.186 Angle : 0.569 6.645 4989 Z= 0.284 Chirality : 0.041 0.164 592 Planarity : 0.004 0.032 618 Dihedral : 4.052 14.938 498 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.60 % Allowed : 14.89 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.40), residues: 465 helix: 1.53 (0.28), residues: 368 sheet: None (None), residues: 0 loop : -0.95 (0.65), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 231 HIS 0.002 0.001 HIS A 377 PHE 0.009 0.001 PHE A 69 TYR 0.007 0.001 TYR A 258 ARG 0.002 0.000 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.321 Fit side-chains REVERT: A 217 GLN cc_start: 0.8006 (mm-40) cc_final: 0.7758 (mm-40) REVERT: A 262 GLU cc_start: -0.0293 (OUTLIER) cc_final: -0.1169 (tp30) outliers start: 6 outliers final: 4 residues processed: 29 average time/residue: 0.1273 time to fit residues: 5.1618 Evaluate side-chains 28 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 23 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 480 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 21 optimal weight: 0.4980 chunk 17 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 36 optimal weight: 0.0270 chunk 23 optimal weight: 10.0000 chunk 26 optimal weight: 0.0970 chunk 16 optimal weight: 0.9980 chunk 14 optimal weight: 0.0000 chunk 5 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 7 optimal weight: 0.0970 overall best weight: 0.1438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 265 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4826 r_free = 0.4826 target = 0.277566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.254954 restraints weight = 3976.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4689 r_free = 0.4689 target = 0.259283 restraints weight = 2367.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4711 r_free = 0.4711 target = 0.262259 restraints weight = 1607.511| |-----------------------------------------------------------------------------| r_work (final): 0.4668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5420 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3655 Z= 0.142 Angle : 0.530 7.851 4989 Z= 0.263 Chirality : 0.040 0.192 592 Planarity : 0.004 0.036 618 Dihedral : 3.871 14.792 498 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.33 % Allowed : 15.69 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.41), residues: 465 helix: 1.82 (0.28), residues: 364 sheet: None (None), residues: 0 loop : -0.69 (0.65), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 231 HIS 0.001 0.000 HIS A 377 PHE 0.011 0.001 PHE A 69 TYR 0.006 0.001 TYR A 327 ARG 0.002 0.000 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 24 time to evaluate : 0.369 Fit side-chains REVERT: A 174 MET cc_start: 0.6288 (mmm) cc_final: 0.5798 (mmm) REVERT: A 211 ILE cc_start: 0.7309 (tp) cc_final: 0.7070 (tt) REVERT: A 262 GLU cc_start: -0.0555 (OUTLIER) cc_final: -0.1170 (tp30) outliers start: 5 outliers final: 3 residues processed: 27 average time/residue: 0.1104 time to fit residues: 4.5284 Evaluate side-chains 27 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 401 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 9 optimal weight: 0.5980 chunk 10 optimal weight: 0.0060 chunk 29 optimal weight: 2.9990 chunk 32 optimal weight: 0.4980 chunk 12 optimal weight: 0.9990 chunk 16 optimal weight: 0.0970 chunk 34 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 3 optimal weight: 0.6980 overall best weight: 0.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 ASN ** 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 = 0.4807 r_free = 0.4807 target = 0.274890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4637 r_free = 0.4637 target = 0.252559 restraints weight = 4020.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4671 r_free = 0.4671 target = 0.256879 restraints weight = 2411.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4693 r_free = 0.4693 target = 0.259878 restraints weight = 1638.477| |-----------------------------------------------------------------------------| r_work (final): 0.4690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5470 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3655 Z= 0.166 Angle : 0.582 12.827 4989 Z= 0.283 Chirality : 0.041 0.193 592 Planarity : 0.004 0.034 618 Dihedral : 3.930 14.596 498 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.60 % Allowed : 15.16 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.41), residues: 465 helix: 1.78 (0.28), residues: 364 sheet: None (None), residues: 0 loop : -0.71 (0.65), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 231 HIS 0.001 0.000 HIS A 377 PHE 0.009 0.001 PHE A 69 TYR 0.005 0.001 TYR A 258 ARG 0.004 0.000 ARG A 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 21 time to evaluate : 0.342 Fit side-chains REVERT: A 211 ILE cc_start: 0.7324 (tp) cc_final: 0.7083 (tt) REVERT: A 262 GLU cc_start: -0.0484 (OUTLIER) cc_final: -0.1232 (tp30) REVERT: A 324 MET cc_start: 0.7269 (mmm) cc_final: 0.6979 (mmm) outliers start: 6 outliers final: 4 residues processed: 26 average time/residue: 0.0845 time to fit residues: 3.6807 Evaluate side-chains 26 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 21 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 401 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 20 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 38 optimal weight: 0.2980 chunk 26 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 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 = 0.4786 r_free = 0.4786 target = 0.272181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.249409 restraints weight = 4023.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.253739 restraints weight = 2449.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.256333 restraints weight = 1680.809| |-----------------------------------------------------------------------------| r_work (final): 0.4662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5533 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3655 Z= 0.190 Angle : 0.597 12.004 4989 Z= 0.292 Chirality : 0.041 0.175 592 Planarity : 0.004 0.032 618 Dihedral : 4.035 14.574 498 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.33 % Allowed : 15.16 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.40), residues: 465 helix: 1.66 (0.28), residues: 363 sheet: None (None), residues: 0 loop : -0.68 (0.64), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 231 HIS 0.002 0.001 HIS A 377 PHE 0.009 0.001 PHE A 426 TYR 0.005 0.001 TYR A 258 ARG 0.004 0.000 ARG A 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1331.60 seconds wall clock time: 23 minutes 57.76 seconds (1437.76 seconds total)