Starting phenix.real_space_refine on Sat Apr 26 21:24:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kb4_37069/04_2025/8kb4_37069_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kb4_37069/04_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_37069/04_2025/8kb4_37069.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kb4_37069/04_2025/8kb4_37069.map" model { file = "/net/cci-nas-00/data/ceres_data/8kb4_37069/04_2025/8kb4_37069_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kb4_37069/04_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-5669/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: 3.47, per 1000 atoms: 1.03 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: 0.89 Conformation dependent library (CDL) restraints added in 370.4 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: 1.04 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: 0.010 Normalize map: mean=0, sd=1: 1.440 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.980 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:3.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.230 ------------------------------------------------------------------------------- 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 : 0.312 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: 0.1206 time to fit residues: 7.4771 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 : 0.362 ------------------------------------------------------------------------------- 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: 0.8980 chunk 31 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 36 optimal weight: 0.0980 chunk 11 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3601 r_free = 0.3601 target = 0.112186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.084901 restraints weight = 5523.671| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 3.27 r_work: 0.3003 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3458 Z= 0.147 Angle : 0.615 6.772 4687 Z= 0.308 Chirality : 0.040 0.168 535 Planarity : 0.004 0.065 555 Dihedral : 17.353 110.050 533 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 0.56 % Allowed : 5.60 % Favored : 93.84 % 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: 2.17 (0.47), residues: 396 helix: 3.74 (0.37), residues: 204 sheet: 0.60 (0.69), residues: 63 loop : -2.22 (0.54), 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 0.012 0.001 PHE A 55 TYR 0.016 0.001 TYR A 340 ARG 0.003 0.001 ARG A 351 Details of bonding type rmsd link_NAG-ASN : bond 0.00447 ( 2) link_NAG-ASN : angle 3.23793 ( 6) hydrogen bonds : bond 0.05088 ( 197) hydrogen bonds : angle 3.39977 ( 576) SS BOND : bond 0.00670 ( 2) SS BOND : angle 1.06977 ( 4) covalent geometry : bond 0.00322 ( 3454) covalent geometry : angle 0.60337 ( 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 : 0.386 Fit side-chains revert: symmetry clash REVERT: A 465 ASN cc_start: 0.9442 (t0) cc_final: 0.9073 (t0) outliers start: 2 outliers final: 1 residues processed: 40 average time/residue: 0.1344 time to fit residues: 7.0209 Evaluate side-chains 35 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 34 time to evaluate : 0.382 ------------------------------------------------------------------------------- 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: 0.8980 chunk 28 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 37 optimal weight: 0.0050 overall best weight: 0.6394 ------------------------------------------------------------------------------- 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 = 0.3614 r_free = 0.3614 target = 0.113063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.085653 restraints weight = 5483.471| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 3.25 r_work: 0.3006 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 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 0.029 3458 Z= 0.123 Angle : 0.575 7.564 4687 Z= 0.280 Chirality : 0.039 0.162 535 Planarity : 0.004 0.064 555 Dihedral : 14.635 103.270 533 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.56 % Allowed : 10.08 % Favored : 89.36 % 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: 2.21 (0.46), residues: 396 helix: 3.73 (0.37), residues: 206 sheet: 0.73 (0.67), residues: 63 loop : -2.31 (0.52), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 42 HIS 0.001 0.001 HIS A 187 PHE 0.011 0.001 PHE A 55 TYR 0.011 0.001 TYR A 340 ARG 0.003 0.000 ARG A 402 Details of bonding type rmsd link_NAG-ASN : bond 0.00419 ( 2) link_NAG-ASN : angle 3.02691 ( 6) hydrogen bonds : bond 0.04577 ( 197) hydrogen bonds : angle 3.18267 ( 576) SS BOND : bond 0.00623 ( 2) SS BOND : angle 1.07852 ( 4) covalent geometry : bond 0.00276 ( 3454) covalent geometry : angle 0.56394 ( 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 39 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 37 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: A 465 ASN cc_start: 0.9477 (t0) cc_final: 0.9099 (t0) outliers start: 2 outliers final: 2 residues processed: 39 average time/residue: 0.1212 time to fit residues: 6.3774 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 : 0.400 ------------------------------------------------------------------------------- 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: 7.9990 chunk 36 optimal weight: 0.3980 chunk 32 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3611 r_free = 0.3611 target = 0.112513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.085089 restraints weight = 5586.910| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 3.29 r_work: 0.3001 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1569 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= 0.130 Angle : 0.563 7.419 4687 Z= 0.273 Chirality : 0.039 0.175 535 Planarity : 0.004 0.063 555 Dihedral : 13.644 97.818 533 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 1.12 % Allowed : 10.92 % Favored : 87.96 % 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: 3.70 (0.36), residues: 206 sheet: 0.79 (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 0.002 0.001 HIS A 187 PHE 0.012 0.001 PHE A 55 TYR 0.011 0.001 TYR A 340 ARG 0.002 0.000 ARG A 257 Details of bonding type rmsd link_NAG-ASN : bond 0.00324 ( 2) link_NAG-ASN : angle 3.21551 ( 6) hydrogen bonds : bond 0.04695 ( 197) hydrogen bonds : angle 3.14178 ( 576) SS BOND : bond 0.00525 ( 2) SS BOND : angle 1.29305 ( 4) covalent geometry : bond 0.00300 ( 3454) covalent geometry : angle 0.55075 ( 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 40 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.396 Fit side-chains REVERT: A 442 ASP cc_start: 0.8751 (m-30) cc_final: 0.8437 (m-30) REVERT: A 465 ASN cc_start: 0.9473 (t0) cc_final: 0.9084 (t0) outliers start: 4 outliers final: 2 residues processed: 39 average time/residue: 0.1103 time to fit residues: 5.8566 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 : 0.374 ------------------------------------------------------------------------------- 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: 1.9990 chunk 18 optimal weight: 0.0010 chunk 1 optimal weight: 0.7980 chunk 22 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.7186 ------------------------------------------------------------------------------- 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 = 0.3611 r_free = 0.3611 target = 0.112639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.085231 restraints weight = 5571.973| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 3.27 r_work: 0.3004 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3458 Z= 0.124 Angle : 0.555 7.503 4687 Z= 0.270 Chirality : 0.038 0.167 535 Planarity : 0.004 0.063 555 Dihedral : 12.718 91.476 533 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.12 % Allowed : 12.61 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.21 (0.46), residues: 396 helix: 3.72 (0.36), residues: 206 sheet: 0.82 (0.67), residues: 63 loop : -2.33 (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 0.011 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 0.00262 ( 2) link_NAG-ASN : angle 3.45033 ( 6) hydrogen bonds : bond 0.04580 ( 197) hydrogen bonds : angle 3.11994 ( 576) SS BOND : bond 0.00560 ( 2) SS BOND : angle 0.66705 ( 4) covalent geometry : bond 0.00283 ( 3454) covalent geometry : angle 0.54156 ( 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 40 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 141 PHE cc_start: 0.7773 (m-80) cc_final: 0.7508 (m-80) REVERT: A 465 ASN cc_start: 0.9481 (t0) cc_final: 0.9083 (t0) outliers start: 4 outliers final: 3 residues processed: 40 average time/residue: 0.1169 time to fit residues: 6.3332 Evaluate side-chains 39 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 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: 1.0382 ------------------------------------------------------------------------------- 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 = 0.3581 r_free = 0.3581 target = 0.110392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.082714 restraints weight = 5706.699| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 3.33 r_work: 0.2954 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3458 Z= 0.157 Angle : 0.575 7.369 4687 Z= 0.283 Chirality : 0.040 0.180 535 Planarity : 0.004 0.062 555 Dihedral : 12.115 90.437 533 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 1.12 % Allowed : 12.89 % Favored : 85.99 % 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: 3.62 (0.36), residues: 206 sheet: 0.81 (0.67), residues: 63 loop : -2.38 (0.50), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 252 HIS 0.002 0.001 HIS A 187 PHE 0.014 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 0.00165 ( 2) link_NAG-ASN : angle 3.35910 ( 6) hydrogen bonds : bond 0.05368 ( 197) hydrogen bonds : angle 3.24304 ( 576) SS BOND : bond 0.00657 ( 2) SS BOND : angle 1.27854 ( 4) covalent geometry : bond 0.00373 ( 3454) covalent geometry : angle 0.56141 ( 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 39 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.377 Fit side-chains REVERT: A 141 PHE cc_start: 0.7855 (m-80) cc_final: 0.7542 (m-80) REVERT: A 441 ASP cc_start: 0.8676 (p0) cc_final: 0.8344 (p0) REVERT: A 442 ASP cc_start: 0.8780 (m-30) cc_final: 0.8475 (m-30) REVERT: A 465 ASN cc_start: 0.9489 (t0) cc_final: 0.9074 (t0) outliers start: 4 outliers final: 3 residues processed: 39 average time/residue: 0.1220 time to fit residues: 6.3867 Evaluate side-chains 34 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.387 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 5 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 29 optimal weight: 0.0470 chunk 22 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 overall best weight: 0.6478 ------------------------------------------------------------------------------- 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 = 0.3608 r_free = 0.3608 target = 0.112319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.084856 restraints weight = 5500.317| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 3.22 r_work: 0.3000 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3458 Z= 0.121 Angle : 0.549 7.533 4687 Z= 0.269 Chirality : 0.038 0.171 535 Planarity : 0.004 0.062 555 Dihedral : 11.688 87.311 533 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.40 % Allowed : 13.45 % 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: 2.10 (0.46), residues: 396 helix: 3.64 (0.37), residues: 206 sheet: 0.80 (0.66), residues: 63 loop : -2.41 (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 171 PHE 0.011 0.001 PHE A 55 TYR 0.014 0.001 TYR A 83 ARG 0.001 0.000 ARG A 402 Details of bonding type rmsd link_NAG-ASN : bond 0.00208 ( 2) link_NAG-ASN : angle 3.59580 ( 6) hydrogen bonds : bond 0.04705 ( 197) hydrogen bonds : angle 3.17054 ( 576) SS BOND : bond 0.00538 ( 2) SS BOND : angle 1.16008 ( 4) covalent geometry : bond 0.00276 ( 3454) covalent geometry : angle 0.53346 ( 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: 5 poor density : 33 time to evaluate : 0.384 Fit side-chains REVERT: A 141 PHE cc_start: 0.7894 (m-80) cc_final: 0.7605 (m-80) REVERT: A 442 ASP cc_start: 0.8774 (m-30) cc_final: 0.8469 (m-30) REVERT: A 465 ASN cc_start: 0.9479 (t0) cc_final: 0.9073 (t0) outliers start: 5 outliers final: 3 residues processed: 38 average time/residue: 0.1187 time to fit residues: 6.1118 Evaluate side-chains 39 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.337 ------------------------------------------------------------------------------- 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: 1.9990 chunk 22 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 10 optimal weight: 0.0170 chunk 21 optimal weight: 0.4980 chunk 4 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 overall best weight: 0.5418 ------------------------------------------------------------------------------- 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 = 0.3614 r_free = 0.3614 target = 0.113093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.085669 restraints weight = 5568.702| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 3.25 r_work: 0.3016 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3458 Z= 0.113 Angle : 0.571 10.118 4687 Z= 0.275 Chirality : 0.040 0.240 535 Planarity : 0.004 0.062 555 Dihedral : 11.202 86.859 533 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.56 % Allowed : 14.85 % 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: 2.14 (0.46), residues: 396 helix: 3.70 (0.37), residues: 206 sheet: 0.76 (0.67), residues: 63 loop : -2.42 (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 171 PHE 0.010 0.001 PHE A 55 TYR 0.015 0.001 TYR A 83 ARG 0.001 0.000 ARG A 402 Details of bonding type rmsd link_NAG-ASN : bond 0.00266 ( 2) link_NAG-ASN : angle 5.70634 ( 6) hydrogen bonds : bond 0.04275 ( 197) hydrogen bonds : angle 3.10423 ( 576) SS BOND : bond 0.00423 ( 2) SS BOND : angle 1.27822 ( 4) covalent geometry : bond 0.00252 ( 3454) covalent geometry : angle 0.53230 ( 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 40 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 38 time to evaluate : 0.397 Fit side-chains REVERT: A 141 PHE cc_start: 0.7906 (m-80) cc_final: 0.7615 (m-80) REVERT: A 441 ASP cc_start: 0.8545 (p0) cc_final: 0.8203 (p0) REVERT: A 442 ASP cc_start: 0.8764 (m-30) cc_final: 0.8451 (m-30) REVERT: A 465 ASN cc_start: 0.9475 (t0) cc_final: 0.9069 (t0) outliers start: 2 outliers final: 2 residues processed: 40 average time/residue: 0.1208 time to fit residues: 6.5958 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 : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 357 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 7.9990 chunk 15 optimal weight: 0.4980 chunk 9 optimal weight: 0.0010 chunk 3 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.6186 ------------------------------------------------------------------------------- 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 = 0.113117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.085654 restraints weight = 5523.357| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 3.26 r_work: 0.3011 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1925 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= 0.119 Angle : 0.584 10.808 4687 Z= 0.277 Chirality : 0.039 0.236 535 Planarity : 0.004 0.062 555 Dihedral : 11.085 90.858 533 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.56 % Allowed : 15.41 % Favored : 84.03 % 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: 0.71 (0.66), residues: 63 loop : -2.45 (0.50), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 82 HIS 0.001 0.001 HIS A 187 PHE 0.011 0.001 PHE A 55 TYR 0.013 0.001 TYR A 83 ARG 0.002 0.000 ARG A 112 Details of bonding type rmsd link_NAG-ASN : bond 0.00601 ( 2) link_NAG-ASN : angle 4.96357 ( 6) hydrogen bonds : bond 0.04363 ( 197) hydrogen bonds : angle 3.09798 ( 576) SS BOND : bond 0.00575 ( 2) SS BOND : angle 0.85310 ( 4) covalent geometry : bond 0.00269 ( 3454) covalent geometry : angle 0.55669 ( 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 39 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 37 time to evaluate : 0.370 Fit side-chains REVERT: A 141 PHE cc_start: 0.7933 (m-80) cc_final: 0.7630 (m-80) REVERT: A 442 ASP cc_start: 0.8747 (m-30) cc_final: 0.8455 (m-30) REVERT: A 465 ASN cc_start: 0.9487 (t0) cc_final: 0.9106 (t0) outliers start: 2 outliers final: 2 residues processed: 39 average time/residue: 0.1132 time to fit residues: 6.0593 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 : 0.384 ------------------------------------------------------------------------------- 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: 0.7980 chunk 39 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 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 = 0.3599 r_free = 0.3599 target = 0.111755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.084421 restraints weight = 5520.593| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 3.24 r_work: 0.2987 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1905 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= 0.141 Angle : 0.587 9.201 4687 Z= 0.283 Chirality : 0.039 0.218 535 Planarity : 0.004 0.061 555 Dihedral : 11.042 93.953 533 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % 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: 2.08 (0.46), residues: 396 helix: 3.67 (0.36), residues: 206 sheet: 0.73 (0.66), residues: 63 loop : -2.47 (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 0.012 0.001 TYR A 83 ARG 0.001 0.000 ARG A 112 Details of bonding type rmsd link_NAG-ASN : bond 0.00513 ( 2) link_NAG-ASN : angle 4.36893 ( 6) hydrogen bonds : bond 0.04912 ( 197) hydrogen bonds : angle 3.18702 ( 576) SS BOND : bond 0.00640 ( 2) SS BOND : angle 0.93937 ( 4) covalent geometry : bond 0.00332 ( 3454) covalent geometry : angle 0.56524 ( 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 41 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.408 Fit side-chains REVERT: A 141 PHE cc_start: 0.7982 (m-80) cc_final: 0.7696 (m-80) REVERT: A 441 ASP cc_start: 0.8560 (p0) cc_final: 0.8245 (p0) REVERT: A 442 ASP cc_start: 0.8718 (m-30) cc_final: 0.8413 (m-30) REVERT: A 465 ASN cc_start: 0.9493 (t0) cc_final: 0.9114 (t0) outliers start: 3 outliers final: 3 residues processed: 41 average time/residue: 0.1185 time to fit residues: 6.6585 Evaluate side-chains 39 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.387 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- 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: 0.7980 chunk 19 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3578 r_free = 0.3578 target = 0.110021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.082507 restraints weight = 5616.276| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 3.28 r_work: 0.2954 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3458 Z= 0.168 Angle : 0.604 9.888 4687 Z= 0.294 Chirality : 0.040 0.211 535 Planarity : 0.004 0.061 555 Dihedral : 11.153 95.628 533 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.12 % Allowed : 15.41 % 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: 1.97 (0.45), residues: 396 helix: 3.56 (0.36), residues: 206 sheet: 0.75 (0.66), residues: 63 loop : -2.55 (0.50), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 252 HIS 0.002 0.001 HIS A 187 PHE 0.014 0.001 PHE A 55 TYR 0.011 0.001 TYR A 83 ARG 0.001 0.000 ARG A 112 Details of bonding type rmsd link_NAG-ASN : bond 0.00471 ( 2) link_NAG-ASN : angle 4.09828 ( 6) hydrogen bonds : bond 0.05581 ( 197) hydrogen bonds : angle 3.32262 ( 576) SS BOND : bond 0.00648 ( 2) SS BOND : angle 1.08901 ( 4) covalent geometry : bond 0.00402 ( 3454) covalent geometry : angle 0.58568 ( 4677) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1869.33 seconds wall clock time: 32 minutes 50.47 seconds (1970.47 seconds total)