Starting phenix.real_space_refine on Fri May 9 18:54:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kb4_37069/05_2025/8kb4_37069_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kb4_37069/05_2025/8kb4_37069.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8kb4_37069/05_2025/8kb4_37069.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kb4_37069/05_2025/8kb4_37069.map" model { file = "/net/cci-nas-00/data/ceres_data/8kb4_37069/05_2025/8kb4_37069_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kb4_37069/05_2025/8kb4_37069_neut_trim.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 20 5.16 5 C 2234 2.51 5 N 535 2.21 5 O 577 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 3367 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3293 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 11, 'TRANS': 390} Chain breaks: 2 Chain: "A" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 74 Unusual residues: {'65I': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.83, per 1000 atoms: 0.84 Number of scatterers: 3367 At special positions: 0 Unit cell: (57.664, 66.992, 112.784, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 20 16.00 P 1 15.00 O 577 8.00 N 535 7.00 C 2234 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS A 128 " distance=2.03 Simple disulfide: pdb=" SG CYS A 89 " - pdb=" SG CYS A 431 " distance=2.04 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 Links applied NAG-ASN " NAG A 901 " - " ASN A 79 " " NAG A 902 " - " ASN A 127 " Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 363.4 milliseconds 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 764 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 2 sheets defined 54.7% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 90 through 95 Processing helix chain 'A' and resid 97 through 99 No H-bonds generated for 'chain 'A' and resid 97 through 99' Processing helix chain 'A' and resid 100 through 110 removed outlier: 4.080A pdb=" N GLU A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 251 Processing helix chain 'A' and resid 256 through 287 removed outlier: 3.501A pdb=" N PHE A 260 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY A 263 " --> pdb=" O GLN A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 318 Processing helix chain 'A' and resid 326 through 331 removed outlier: 4.259A pdb=" N LEU A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 337 Processing helix chain 'A' and resid 338 through 354 removed outlier: 4.198A pdb=" N LEU A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE A 343 " --> pdb=" O LEU A 339 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU A 350 " --> pdb=" O MET A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 393 removed outlier: 4.277A pdb=" N LEU A 367 " --> pdb=" O ALA A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 427 removed outlier: 3.643A pdb=" N SER A 399 " --> pdb=" O ILE A 395 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU A 400 " --> pdb=" O VAL A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 442 Processing helix chain 'A' and resid 443 through 460 Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 44 removed outlier: 3.713A pdb=" N ASP A 70 " --> pdb=" O THR A 207 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 59 removed outlier: 3.974A pdb=" N SER A 77 " --> pdb=" O SER A 191 " (cutoff:3.500A) 197 hydrogen bonds defined for protein. 576 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: 0.88 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 493 1.31 - 1.43: 1013 1.43 - 1.56: 1913 1.56 - 1.69: 2 1.69 - 1.81: 33 Bond restraints: 3454 Sorted by residual: bond pdb=" C11 65I A 903 " pdb=" O6 65I A 903 " ideal model delta sigma weight residual 1.331 1.400 -0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" C5 65I A 903 " pdb=" O1 65I A 903 " ideal model delta sigma weight residual 1.335 1.400 -0.065 2.00e-02 2.50e+03 1.05e+01 bond pdb=" C1 NAG A 902 " pdb=" O5 NAG A 902 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.81e+00 bond pdb=" C7 65I A 903 " pdb=" O6 65I A 903 " ideal model delta sigma weight residual 1.429 1.399 0.030 2.00e-02 2.50e+03 2.25e+00 bond pdb=" C6 65I A 903 " pdb=" O1 65I A 903 " ideal model delta sigma weight residual 1.427 1.399 0.028 2.00e-02 2.50e+03 1.95e+00 ... (remaining 3449 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.33: 4666 4.33 - 8.67: 7 8.67 - 13.00: 3 13.00 - 17.34: 0 17.34 - 21.67: 1 Bond angle restraints: 4677 Sorted by residual: angle pdb=" C17 65I A 903 " pdb=" C18 65I A 903 " pdb=" C19 65I A 903 " ideal model delta sigma weight residual 114.14 135.81 -21.67 3.00e+00 1.11e-01 5.22e+01 angle pdb=" C THR A 357 " pdb=" N ASP A 358 " pdb=" CA ASP A 358 " ideal model delta sigma weight residual 122.61 130.38 -7.77 1.56e+00 4.11e-01 2.48e+01 angle pdb=" O3 65I A 903 " pdb=" P 65I A 903 " pdb=" O4 65I A 903 " ideal model delta sigma weight residual 122.02 109.40 12.62 3.00e+00 1.11e-01 1.77e+01 angle pdb=" O2 65I A 903 " pdb=" P 65I A 903 " pdb=" O5 65I A 903 " ideal model delta sigma weight residual 98.05 109.63 -11.58 3.00e+00 1.11e-01 1.49e+01 angle pdb=" N ASP A 75 " pdb=" CA ASP A 75 " pdb=" C ASP A 75 " ideal model delta sigma weight residual 113.18 108.39 4.79 1.33e+00 5.65e-01 1.30e+01 ... (remaining 4672 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.61: 1924 25.61 - 51.22: 112 51.22 - 76.82: 18 76.82 - 102.43: 9 102.43 - 128.04: 6 Dihedral angle restraints: 2069 sinusoidal: 889 harmonic: 1180 Sorted by residual: dihedral pdb=" CB CYS A 74 " pdb=" SG CYS A 74 " pdb=" SG CYS A 128 " pdb=" CB CYS A 128 " ideal model delta sinusoidal sigma weight residual -86.00 -37.98 -48.02 1 1.00e+01 1.00e-02 3.18e+01 dihedral pdb=" C2 65I A 903 " pdb=" C3 65I A 903 " pdb=" C4 65I A 903 " pdb=" C5 65I A 903 " ideal model delta sinusoidal sigma weight residual -173.23 -45.19 -128.04 1 3.00e+01 1.11e-03 1.72e+01 dihedral pdb=" C2 NAG A 902 " pdb=" C1 NAG A 902 " pdb=" O5 NAG A 902 " pdb=" C5 NAG A 902 " ideal model delta sinusoidal sigma weight residual -62.96 60.58 -123.54 1 3.00e+01 1.11e-03 1.66e+01 ... (remaining 2066 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 361 0.031 - 0.062: 127 0.062 - 0.092: 32 0.092 - 0.123: 10 0.123 - 0.154: 5 Chirality restraints: 535 Sorted by residual: chirality pdb=" C1 NAG A 902 " pdb=" ND2 ASN A 127 " pdb=" C2 NAG A 902 " pdb=" O5 NAG A 902 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-01 2.50e+01 5.91e-01 chirality pdb=" CA ILE A 183 " pdb=" N ILE A 183 " pdb=" C ILE A 183 " pdb=" CB ILE A 183 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.50e-01 chirality pdb=" CA ASP A 358 " pdb=" N ASP A 358 " pdb=" C ASP A 358 " pdb=" CB ASP A 358 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.23e-01 ... (remaining 532 not shown) Planarity restraints: 557 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 72 " -0.031 5.00e-02 4.00e+02 4.79e-02 3.67e+00 pdb=" N PRO A 73 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 73 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 73 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 357 " -0.008 2.00e-02 2.50e+03 1.68e-02 2.82e+00 pdb=" C THR A 357 " 0.029 2.00e-02 2.50e+03 pdb=" O THR A 357 " -0.011 2.00e-02 2.50e+03 pdb=" N ASP A 358 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 221 " -0.005 2.00e-02 2.50e+03 9.91e-03 9.81e-01 pdb=" C LEU A 221 " 0.017 2.00e-02 2.50e+03 pdb=" O LEU A 221 " -0.006 2.00e-02 2.50e+03 pdb=" N GLU A 222 " -0.006 2.00e-02 2.50e+03 ... (remaining 554 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 77 2.70 - 3.25: 3391 3.25 - 3.80: 5040 3.80 - 4.35: 5860 4.35 - 4.90: 10338 Nonbonded interactions: 24706 Sorted by model distance: nonbonded pdb=" N GLU A 217 " pdb=" OE1 GLU A 217 " model vdw 2.151 3.120 nonbonded pdb=" O THR A 357 " pdb=" OD1 ASP A 358 " model vdw 2.207 3.040 nonbonded pdb=" N GLY A 71 " pdb=" OE2 GLU A 130 " model vdw 2.231 3.120 nonbonded pdb=" O GLN A 178 " pdb=" OH TYR A 182 " model vdw 2.256 3.040 nonbonded pdb=" OD1 ASN A 91 " pdb=" N GLU A 92 " model vdw 2.266 3.120 ... (remaining 24701 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: 1.050 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.800 Find NCS groups from input model: 0.030 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 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 0.069 3458 Z= 0.201 Angle : 0.705 21.673 4687 Z= 0.323 Chirality : 0.037 0.154 535 Planarity : 0.003 0.048 555 Dihedral : 19.096 128.040 1299 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 19.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % 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: 1.68 (0.47), residues: 396 helix: 3.28 (0.38), residues: 204 sheet: 0.04 (0.68), residues: 67 loop : -2.19 (0.54), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 247 HIS 0.002 0.001 HIS A 171 PHE 0.010 0.001 PHE A 379 TYR 0.009 0.001 TYR A 104 ARG 0.001 0.000 ARG A 39 Details of bonding type rmsd link_NAG-ASN : bond 0.00262 ( 2) link_NAG-ASN : angle 1.36210 ( 6) hydrogen bonds : bond 0.12354 ( 197) hydrogen bonds : angle 5.00491 ( 576) SS BOND : bond 0.00600 ( 2) SS BOND : angle 0.93104 ( 4) covalent geometry : bond 0.00436 ( 3454) covalent geometry : angle 0.70339 ( 4677) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: A 434 ASP cc_start: 0.8624 (p0) cc_final: 0.8414 (p0) REVERT: A 465 ASN cc_start: 0.9337 (t0) cc_final: 0.9035 (t0) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.1160 time to fit residues: 7.2525 Evaluate side-chains 40 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 466 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.111860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.084450 restraints weight = 5541.729| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 3.29 r_work: 0.2989 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3458 Z= 0.145 Angle : 0.617 6.500 4687 Z= 0.308 Chirality : 0.040 0.174 535 Planarity : 0.005 0.064 555 Dihedral : 17.369 109.370 533 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.56 % Allowed : 5.32 % Favored : 94.12 % 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: 2.12 (0.47), residues: 396 helix: 3.69 (0.37), residues: 204 sheet: 0.61 (0.69), residues: 63 loop : -2.24 (0.53), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 247 HIS 0.003 0.001 HIS A 171 PHE 0.013 0.001 PHE A 55 TYR 0.016 0.002 TYR A 340 ARG 0.003 0.001 ARG A 351 Details of bonding type rmsd link_NAG-ASN : bond 0.00514 ( 2) link_NAG-ASN : angle 3.20791 ( 6) hydrogen bonds : bond 0.05240 ( 197) hydrogen bonds : angle 3.42166 ( 576) SS BOND : bond 0.00831 ( 2) SS BOND : angle 1.20318 ( 4) covalent geometry : bond 0.00332 ( 3454) covalent geometry : angle 0.60611 ( 4677) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 38 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: A 465 ASN cc_start: 0.9448 (t0) cc_final: 0.9076 (t0) outliers start: 2 outliers final: 1 residues processed: 40 average time/residue: 0.1408 time to fit residues: 7.2543 Evaluate side-chains 34 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 444 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 15 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 13 optimal weight: 0.0050 chunk 38 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 11 optimal weight: 0.0020 chunk 6 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 overall best weight: 0.5602 ------------------------------------------------------------------------------- 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 = 0.3618 r_free = 0.3618 target = 0.113339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.085940 restraints weight = 5482.508| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 3.24 r_work: 0.3012 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3458 Z= 0.119 Angle : 0.575 7.605 4687 Z= 0.281 Chirality : 0.039 0.163 535 Planarity : 0.004 0.064 555 Dihedral : 14.817 103.792 533 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.56 % Allowed : 9.80 % Favored : 89.64 % 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: 2.19 (0.46), residues: 396 helix: 3.72 (0.37), residues: 206 sheet: 0.70 (0.67), residues: 63 loop : -2.32 (0.52), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 42 HIS 0.002 0.001 HIS A 171 PHE 0.010 0.001 PHE A 55 TYR 0.012 0.001 TYR A 90 ARG 0.003 0.000 ARG A 402 Details of bonding type rmsd link_NAG-ASN : bond 0.00433 ( 2) link_NAG-ASN : angle 3.09079 ( 6) hydrogen bonds : bond 0.04503 ( 197) hydrogen bonds : angle 3.17256 ( 576) SS BOND : bond 0.01090 ( 2) SS BOND : angle 1.01419 ( 4) covalent geometry : bond 0.00261 ( 3454) covalent geometry : angle 0.56375 ( 4677) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.344 Fit side-chains REVERT: A 442 ASP cc_start: 0.8735 (m-30) cc_final: 0.8420 (m-30) REVERT: A 465 ASN cc_start: 0.9478 (t0) cc_final: 0.9101 (t0) outliers start: 2 outliers final: 2 residues processed: 36 average time/residue: 0.1202 time to fit residues: 5.8362 Evaluate side-chains 38 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 36 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 444 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 7 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 39 optimal weight: 0.0870 chunk 11 optimal weight: 2.9990 overall best weight: 0.8960 ------------------------------------------------------------------------------- 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 = 0.3586 r_free = 0.3586 target = 0.111093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.083761 restraints weight = 5619.808| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 3.19 r_work: 0.3001 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3458 Z= 0.143 Angle : 0.572 7.416 4687 Z= 0.279 Chirality : 0.039 0.168 535 Planarity : 0.004 0.064 555 Dihedral : 13.619 97.885 533 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.84 % Allowed : 10.64 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.13 (0.46), residues: 396 helix: 3.65 (0.36), residues: 206 sheet: 0.82 (0.67), residues: 63 loop : -2.37 (0.51), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 82 HIS 0.002 0.001 HIS A 187 PHE 0.013 0.001 PHE A 55 TYR 0.011 0.001 TYR A 340 ARG 0.002 0.000 ARG A 402 Details of bonding type rmsd link_NAG-ASN : bond 0.00309 ( 2) link_NAG-ASN : angle 3.17089 ( 6) hydrogen bonds : bond 0.05029 ( 197) hydrogen bonds : angle 3.19890 ( 576) SS BOND : bond 0.00640 ( 2) SS BOND : angle 1.24062 ( 4) covalent geometry : bond 0.00336 ( 3454) covalent geometry : angle 0.55960 ( 4677) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.410 Fit side-chains REVERT: A 442 ASP cc_start: 0.8746 (m-30) cc_final: 0.8434 (m-30) REVERT: A 465 ASN cc_start: 0.9475 (t0) cc_final: 0.9083 (t0) outliers start: 3 outliers final: 2 residues processed: 38 average time/residue: 0.1189 time to fit residues: 5.9808 Evaluate side-chains 36 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 444 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 6 optimal weight: 0.7980 chunk 18 optimal weight: 0.0870 chunk 1 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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 = 0.3620 r_free = 0.3620 target = 0.113172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.085703 restraints weight = 5551.578| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 3.27 r_work: 0.3006 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3458 Z= 0.114 Angle : 0.547 7.532 4687 Z= 0.266 Chirality : 0.038 0.166 535 Planarity : 0.004 0.063 555 Dihedral : 12.801 91.500 533 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.56 % Allowed : 12.61 % Favored : 86.83 % 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: 2.23 (0.46), residues: 396 helix: 3.74 (0.37), residues: 206 sheet: 0.82 (0.67), residues: 63 loop : -2.32 (0.51), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 82 HIS 0.001 0.001 HIS A 187 PHE 0.010 0.001 PHE A 55 TYR 0.011 0.001 TYR A 340 ARG 0.002 0.000 ARG A 402 Details of bonding type rmsd link_NAG-ASN : bond 0.00292 ( 2) link_NAG-ASN : angle 3.51170 ( 6) hydrogen bonds : bond 0.04436 ( 197) hydrogen bonds : angle 3.10375 ( 576) SS BOND : bond 0.00569 ( 2) SS BOND : angle 0.96041 ( 4) covalent geometry : bond 0.00255 ( 3454) covalent geometry : angle 0.53260 ( 4677) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 36 time to evaluate : 0.317 Fit side-chains revert: symmetry clash REVERT: A 141 PHE cc_start: 0.7762 (m-80) cc_final: 0.7484 (m-80) REVERT: A 465 ASN cc_start: 0.9481 (t0) cc_final: 0.9085 (t0) outliers start: 2 outliers final: 2 residues processed: 38 average time/residue: 0.1129 time to fit residues: 5.8209 Evaluate side-chains 38 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 36 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 357 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 2.9990 chunk 32 optimal weight: 0.0060 chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.8998 ------------------------------------------------------------------------------- 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 = 0.3595 r_free = 0.3595 target = 0.111361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.083292 restraints weight = 5691.485| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 3.34 r_work: 0.2971 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3458 Z= 0.140 Angle : 0.559 7.448 4687 Z= 0.274 Chirality : 0.039 0.176 535 Planarity : 0.004 0.062 555 Dihedral : 12.197 90.353 533 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 1.68 % Allowed : 13.17 % Favored : 85.15 % 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: 2.15 (0.46), residues: 396 helix: 3.68 (0.36), residues: 206 sheet: 0.83 (0.67), residues: 63 loop : -2.38 (0.50), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 82 HIS 0.002 0.001 HIS A 187 PHE 0.013 0.001 PHE A 55 TYR 0.010 0.001 TYR A 340 ARG 0.001 0.000 ARG A 112 Details of bonding type rmsd link_NAG-ASN : bond 0.00189 ( 2) link_NAG-ASN : angle 3.42816 ( 6) hydrogen bonds : bond 0.04985 ( 197) hydrogen bonds : angle 3.18296 ( 576) SS BOND : bond 0.00647 ( 2) SS BOND : angle 1.13766 ( 4) covalent geometry : bond 0.00329 ( 3454) covalent geometry : angle 0.54540 ( 4677) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.379 Fit side-chains REVERT: A 141 PHE cc_start: 0.7833 (m-80) cc_final: 0.7515 (m-80) REVERT: A 442 ASP cc_start: 0.8749 (m-30) cc_final: 0.8451 (m-30) REVERT: A 465 ASN cc_start: 0.9489 (t0) cc_final: 0.9079 (t0) outliers start: 6 outliers final: 4 residues processed: 41 average time/residue: 0.1239 time to fit residues: 6.8342 Evaluate side-chains 39 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 444 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 5 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 25 optimal weight: 0.0970 chunk 34 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- 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 = 0.3603 r_free = 0.3603 target = 0.112083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.084522 restraints weight = 5526.820| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 3.27 r_work: 0.2997 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3458 Z= 0.126 Angle : 0.553 7.524 4687 Z= 0.271 Chirality : 0.038 0.172 535 Planarity : 0.004 0.062 555 Dihedral : 11.829 87.989 533 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.12 % Allowed : 14.01 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.11 (0.46), residues: 396 helix: 3.64 (0.37), residues: 206 sheet: 0.83 (0.66), residues: 63 loop : -2.40 (0.50), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 82 HIS 0.002 0.001 HIS A 171 PHE 0.011 0.001 PHE A 55 TYR 0.011 0.001 TYR A 340 ARG 0.001 0.000 ARG A 112 Details of bonding type rmsd link_NAG-ASN : bond 0.00202 ( 2) link_NAG-ASN : angle 3.56434 ( 6) hydrogen bonds : bond 0.04687 ( 197) hydrogen bonds : angle 3.17105 ( 576) SS BOND : bond 0.00532 ( 2) SS BOND : angle 1.14638 ( 4) covalent geometry : bond 0.00289 ( 3454) covalent geometry : angle 0.53727 ( 4677) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.350 Fit side-chains REVERT: A 141 PHE cc_start: 0.7886 (m-80) cc_final: 0.7590 (m-80) REVERT: A 441 ASP cc_start: 0.8566 (p0) cc_final: 0.8210 (p0) REVERT: A 442 ASP cc_start: 0.8754 (m-30) cc_final: 0.8439 (m-30) REVERT: A 465 ASN cc_start: 0.9482 (t0) cc_final: 0.9074 (t0) outliers start: 4 outliers final: 3 residues processed: 38 average time/residue: 0.1177 time to fit residues: 6.0344 Evaluate side-chains 40 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 444 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 chunk 15 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3589 r_free = 0.3589 target = 0.111150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.083765 restraints weight = 5594.542| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 3.27 r_work: 0.2974 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3458 Z= 0.141 Angle : 0.576 8.840 4687 Z= 0.281 Chirality : 0.040 0.245 535 Planarity : 0.004 0.062 555 Dihedral : 11.540 88.922 533 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.84 % Allowed : 14.57 % Favored : 84.59 % 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: 2.08 (0.46), residues: 396 helix: 3.60 (0.36), residues: 206 sheet: 0.83 (0.66), residues: 63 loop : -2.42 (0.50), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 82 HIS 0.002 0.001 HIS A 187 PHE 0.012 0.001 PHE A 55 TYR 0.010 0.001 TYR A 340 ARG 0.001 0.000 ARG A 112 Details of bonding type rmsd link_NAG-ASN : bond 0.00487 ( 2) link_NAG-ASN : angle 5.04684 ( 6) hydrogen bonds : bond 0.04952 ( 197) hydrogen bonds : angle 3.19056 ( 576) SS BOND : bond 0.00531 ( 2) SS BOND : angle 1.34997 ( 4) covalent geometry : bond 0.00331 ( 3454) covalent geometry : angle 0.54643 ( 4677) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.388 Fit side-chains REVERT: A 141 PHE cc_start: 0.7929 (m-80) cc_final: 0.7613 (m-80) REVERT: A 442 ASP cc_start: 0.8721 (m-30) cc_final: 0.8434 (m-30) REVERT: A 465 ASN cc_start: 0.9487 (t0) cc_final: 0.9072 (t0) outliers start: 3 outliers final: 3 residues processed: 42 average time/residue: 0.1205 time to fit residues: 6.8385 Evaluate side-chains 38 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 444 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.2980 chunk 15 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 36 optimal weight: 0.0570 chunk 19 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.5298 ------------------------------------------------------------------------------- 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 = 0.3616 r_free = 0.3616 target = 0.112823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.085298 restraints weight = 5517.815| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 3.24 r_work: 0.3005 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3458 Z= 0.115 Angle : 0.563 9.066 4687 Z= 0.274 Chirality : 0.039 0.239 535 Planarity : 0.004 0.063 555 Dihedral : 11.244 89.165 533 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.56 % Allowed : 15.69 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.13 (0.46), residues: 396 helix: 3.71 (0.37), residues: 206 sheet: 0.76 (0.66), residues: 63 loop : -2.46 (0.50), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 82 HIS 0.001 0.001 HIS A 187 PHE 0.010 0.001 PHE A 55 TYR 0.013 0.001 TYR A 83 ARG 0.001 0.000 ARG A 402 Details of bonding type rmsd link_NAG-ASN : bond 0.00648 ( 2) link_NAG-ASN : angle 5.04090 ( 6) hydrogen bonds : bond 0.04379 ( 197) hydrogen bonds : angle 3.10030 ( 576) SS BOND : bond 0.00583 ( 2) SS BOND : angle 0.89393 ( 4) covalent geometry : bond 0.00256 ( 3454) covalent geometry : angle 0.53350 ( 4677) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.394 Fit side-chains REVERT: A 141 PHE cc_start: 0.7914 (m-80) cc_final: 0.7599 (m-80) REVERT: A 441 ASP cc_start: 0.8534 (p0) cc_final: 0.8204 (p0) REVERT: A 442 ASP cc_start: 0.8725 (m-30) cc_final: 0.8416 (m-30) REVERT: A 465 ASN cc_start: 0.9484 (t0) cc_final: 0.9102 (t0) outliers start: 2 outliers final: 2 residues processed: 42 average time/residue: 0.1172 time to fit residues: 6.6699 Evaluate side-chains 41 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 39 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 357 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3600 r_free = 0.3600 target = 0.111845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.084216 restraints weight = 5505.668| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 3.26 r_work: 0.2991 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3458 Z= 0.135 Angle : 0.585 10.056 4687 Z= 0.280 Chirality : 0.040 0.224 535 Planarity : 0.004 0.062 555 Dihedral : 11.149 92.062 533 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.56 % Allowed : 15.97 % Favored : 83.47 % 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: 2.08 (0.46), residues: 396 helix: 3.67 (0.37), residues: 206 sheet: 0.74 (0.65), residues: 63 loop : -2.49 (0.50), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 82 HIS 0.002 0.001 HIS A 187 PHE 0.012 0.001 PHE A 55 TYR 0.014 0.001 TYR A 83 ARG 0.001 0.000 ARG A 112 Details of bonding type rmsd link_NAG-ASN : bond 0.00556 ( 2) link_NAG-ASN : angle 4.54687 ( 6) hydrogen bonds : bond 0.04767 ( 197) hydrogen bonds : angle 3.16862 ( 576) SS BOND : bond 0.00507 ( 2) SS BOND : angle 0.94490 ( 4) covalent geometry : bond 0.00318 ( 3454) covalent geometry : angle 0.56234 ( 4677) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 38 time to evaluate : 0.370 Fit side-chains REVERT: A 141 PHE cc_start: 0.7950 (m-80) cc_final: 0.7634 (m-80) REVERT: A 441 ASP cc_start: 0.8548 (p0) cc_final: 0.8223 (p0) REVERT: A 442 ASP cc_start: 0.8723 (m-30) cc_final: 0.8415 (m-30) REVERT: A 465 ASN cc_start: 0.9484 (t0) cc_final: 0.9104 (t0) outliers start: 2 outliers final: 2 residues processed: 40 average time/residue: 0.1202 time to fit residues: 6.5017 Evaluate side-chains 39 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 37 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 357 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 28 optimal weight: 7.9990 chunk 18 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3590 r_free = 0.3590 target = 0.110879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.083428 restraints weight = 5594.199| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 3.27 r_work: 0.2971 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3458 Z= 0.149 Angle : 0.590 9.344 4687 Z= 0.286 Chirality : 0.040 0.210 535 Planarity : 0.004 0.062 555 Dihedral : 11.103 95.107 533 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.84 % Allowed : 16.25 % Favored : 82.91 % 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: 2.02 (0.46), residues: 396 helix: 3.62 (0.36), residues: 206 sheet: 0.75 (0.66), residues: 63 loop : -2.53 (0.49), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 82 HIS 0.002 0.001 HIS A 187 PHE 0.013 0.001 PHE A 55 TYR 0.014 0.001 TYR A 83 ARG 0.001 0.000 ARG A 112 Details of bonding type rmsd link_NAG-ASN : bond 0.00505 ( 2) link_NAG-ASN : angle 4.21795 ( 6) hydrogen bonds : bond 0.05160 ( 197) hydrogen bonds : angle 3.24304 ( 576) SS BOND : bond 0.00567 ( 2) SS BOND : angle 1.01991 ( 4) covalent geometry : bond 0.00352 ( 3454) covalent geometry : angle 0.57011 ( 4677) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1838.04 seconds wall clock time: 32 minutes 39.31 seconds (1959.31 seconds total)