Starting phenix.real_space_refine on Sat May 10 00:32:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y7z_33675/05_2025/7y7z_33675.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y7z_33675/05_2025/7y7z_33675.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y7z_33675/05_2025/7y7z_33675.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y7z_33675/05_2025/7y7z_33675.map" model { file = "/net/cci-nas-00/data/ceres_data/7y7z_33675/05_2025/7y7z_33675.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y7z_33675/05_2025/7y7z_33675.cif" } resolution = 3.2 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= 0.002 sd= 0.130 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 S 36 5.16 5 Cl 1 4.86 5 C 2876 2.51 5 N 661 2.21 5 O 729 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 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: 4303 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4235 Classifications: {'peptide': 532} Link IDs: {'PTRANS': 23, 'TRANS': 508} Chain: "A" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 68 Unusual residues: {' CL': 1, 'NAG': 3, 'TGI': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.14, per 1000 atoms: 0.73 Number of scatterers: 4303 At special positions: 0 Unit cell: (71.445, 74.6925, 96.3425, 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) Cl 1 17.00 S 36 16.00 O 729 8.00 N 661 7.00 C 2876 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 164 " - pdb=" SG CYS A 173 " distance=2.02 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 702 " - " ASN A 181 " " NAG A 703 " - " ASN A 176 " " NAG A 704 " - " ASN A 184 " Time building additional restraints: 1.21 Conformation dependent library (CDL) restraints added in 600.0 milliseconds 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 972 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 2 sheets defined 77.4% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 49 through 60 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.643A pdb=" N VAL A 67 " --> pdb=" O GLY A 63 " (cutoff:3.500A) Proline residue: A 71 - end of helix Processing helix chain 'A' and resid 79 through 81 No H-bonds generated for 'chain 'A' and resid 79 through 81' Processing helix chain 'A' and resid 82 through 93 Processing helix chain 'A' and resid 94 through 109 Processing helix chain 'A' and resid 119 through 122 Processing helix chain 'A' and resid 123 through 155 removed outlier: 3.764A pdb=" N LEU A 127 " --> pdb=" O LYS A 123 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE A 155 " --> pdb=" O LEU A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 197 Processing helix chain 'A' and resid 211 through 230 Processing helix chain 'A' and resid 234 through 238 removed outlier: 3.946A pdb=" N GLY A 237 " --> pdb=" O GLY A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 260 removed outlier: 3.895A pdb=" N THR A 260 " --> pdb=" O PHE A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 273 removed outlier: 3.660A pdb=" N GLY A 267 " --> pdb=" O GLY A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 296 removed outlier: 3.901A pdb=" N TRP A 285 " --> pdb=" O ASP A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 310 removed outlier: 4.157A pdb=" N ALA A 305 " --> pdb=" O GLY A 301 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN A 310 " --> pdb=" O LEU A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 350 removed outlier: 3.518A pdb=" N GLY A 343 " --> pdb=" O PHE A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 358 Processing helix chain 'A' and resid 363 through 374 removed outlier: 3.511A pdb=" N TYR A 368 " --> pdb=" O ALA A 364 " (cutoff:3.500A) Proline residue: A 369 - end of helix Processing helix chain 'A' and resid 377 through 412 removed outlier: 3.668A pdb=" N TRP A 381 " --> pdb=" O ILE A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 417 Processing helix chain 'A' and resid 419 through 439 Processing helix chain 'A' and resid 442 through 454 removed outlier: 4.315A pdb=" N VAL A 446 " --> pdb=" O GLY A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 474 removed outlier: 3.676A pdb=" N PHE A 465 " --> pdb=" O LEU A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 489 Processing helix chain 'A' and resid 493 through 519 removed outlier: 4.511A pdb=" N LYS A 497 " --> pdb=" O CYS A 493 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N THR A 504 " --> pdb=" O TRP A 500 " (cutoff:3.500A) Proline residue: A 505 - end of helix removed outlier: 3.527A pdb=" N GLN A 518 " --> pdb=" O PHE A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 546 Processing helix chain 'A' and resid 546 through 559 removed outlier: 3.749A pdb=" N LEU A 559 " --> pdb=" O MET A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 572 Processing sheet with id=AA1, first strand: chain 'A' and resid 173 through 174 removed outlier: 3.565A pdb=" N PHE A 174 " --> pdb=" O THR A 186 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 523 through 524 282 hydrogen bonds defined for protein. 837 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: 1.08 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 648 1.32 - 1.45: 1359 1.45 - 1.57: 2375 1.57 - 1.69: 0 1.69 - 1.81: 58 Bond restraints: 4440 Sorted by residual: bond pdb=" C17 TGI A 701 " pdb=" O19 TGI A 701 " ideal model delta sigma weight residual 1.261 1.203 0.058 2.00e-02 2.50e+03 8.37e+00 bond pdb=" C20 TGI A 701 " pdb=" C21 TGI A 701 " ideal model delta sigma weight residual 1.374 1.430 -0.056 2.00e-02 2.50e+03 7.91e+00 bond pdb=" C17 TGI A 701 " pdb=" O18 TGI A 701 " ideal model delta sigma weight residual 1.260 1.204 0.056 2.00e-02 2.50e+03 7.80e+00 bond pdb=" N VAL A 323 " pdb=" CA VAL A 323 " ideal model delta sigma weight residual 1.461 1.492 -0.030 1.17e-02 7.31e+03 6.73e+00 bond pdb=" C02 TGI A 701 " pdb=" C03 TGI A 701 " ideal model delta sigma weight residual 1.380 1.423 -0.043 2.00e-02 2.50e+03 4.57e+00 ... (remaining 4435 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.15: 5561 1.15 - 2.30: 382 2.30 - 3.45: 71 3.45 - 4.59: 27 4.59 - 5.74: 8 Bond angle restraints: 6049 Sorted by residual: angle pdb=" CA TYR A 60 " pdb=" CB TYR A 60 " pdb=" CG TYR A 60 " ideal model delta sigma weight residual 113.90 119.64 -5.74 1.80e+00 3.09e-01 1.02e+01 angle pdb=" C ILE A 138 " pdb=" N TYR A 139 " pdb=" CA TYR A 139 " ideal model delta sigma weight residual 121.14 115.83 5.31 1.75e+00 3.27e-01 9.22e+00 angle pdb=" CA VAL A 323 " pdb=" C VAL A 323 " pdb=" O VAL A 323 " ideal model delta sigma weight residual 121.17 118.28 2.89 1.06e+00 8.90e-01 7.43e+00 angle pdb=" O VAL A 323 " pdb=" C VAL A 323 " pdb=" N CYS A 324 " ideal model delta sigma weight residual 121.91 124.44 -2.53 9.80e-01 1.04e+00 6.67e+00 angle pdb=" CA TYR A 139 " pdb=" CB TYR A 139 " pdb=" CG TYR A 139 " ideal model delta sigma weight residual 113.90 118.46 -4.56 1.80e+00 3.09e-01 6.41e+00 ... (remaining 6044 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.49: 2287 20.49 - 40.98: 252 40.98 - 61.47: 16 61.47 - 81.96: 2 81.96 - 102.45: 2 Dihedral angle restraints: 2559 sinusoidal: 1027 harmonic: 1532 Sorted by residual: dihedral pdb=" CA SER A 456 " pdb=" C SER A 456 " pdb=" N GLY A 457 " pdb=" CA GLY A 457 " ideal model delta harmonic sigma weight residual -180.00 -157.18 -22.82 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA PHE A 339 " pdb=" C PHE A 339 " pdb=" N SER A 340 " pdb=" CA SER A 340 " ideal model delta harmonic sigma weight residual 180.00 158.37 21.63 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA TRP A 116 " pdb=" C TRP A 116 " pdb=" N LYS A 117 " pdb=" CA LYS A 117 " ideal model delta harmonic sigma weight residual 180.00 158.74 21.26 0 5.00e+00 4.00e-02 1.81e+01 ... (remaining 2556 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 512 0.049 - 0.099: 129 0.099 - 0.148: 27 0.148 - 0.198: 2 0.198 - 0.247: 1 Chirality restraints: 671 Sorted by residual: chirality pdb=" C1 NAG A 703 " pdb=" ND2 ASN A 176 " pdb=" C2 NAG A 703 " pdb=" O5 NAG A 703 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA VAL A 323 " pdb=" N VAL A 323 " pdb=" C VAL A 323 " pdb=" CB VAL A 323 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.28e-01 chirality pdb=" C1 NAG A 702 " pdb=" ND2 ASN A 181 " pdb=" C2 NAG A 702 " pdb=" O5 NAG A 702 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-01 2.50e+01 6.74e-01 ... (remaining 668 not shown) Planarity restraints: 736 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 184 " 0.219 2.00e-02 2.50e+03 2.83e-01 1.00e+03 pdb=" CG ASN A 184 " -0.091 2.00e-02 2.50e+03 pdb=" OD1 ASN A 184 " 0.022 2.00e-02 2.50e+03 pdb=" ND2 ASN A 184 " -0.483 2.00e-02 2.50e+03 pdb=" C1 NAG A 704 " 0.333 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C03 TGI A 701 " 0.009 2.00e-02 2.50e+03 1.80e-01 4.05e+02 pdb=" C07 TGI A 701 " 0.042 2.00e-02 2.50e+03 pdb=" C08 TGI A 701 " 0.307 2.00e-02 2.50e+03 pdb=" C09 TGI A 701 " -0.210 2.00e-02 2.50e+03 pdb=" C20 TGI A 701 " -0.148 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 176 " -0.099 2.00e-02 2.50e+03 1.58e-01 3.11e+02 pdb=" CG ASN A 176 " 0.045 2.00e-02 2.50e+03 pdb=" OD1 ASN A 176 " -0.055 2.00e-02 2.50e+03 pdb=" ND2 ASN A 176 " 0.282 2.00e-02 2.50e+03 pdb=" C1 NAG A 703 " -0.173 2.00e-02 2.50e+03 ... (remaining 733 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 38 2.61 - 3.18: 4047 3.18 - 3.75: 6585 3.75 - 4.33: 8993 4.33 - 4.90: 15408 Nonbonded interactions: 35071 Sorted by model distance: nonbonded pdb=" OG1 THR A 170 " pdb=" OE2 GLU A 191 " model vdw 2.037 3.040 nonbonded pdb=" O GLY A 561 " pdb=" NH1 ARG A 566 " model vdw 2.119 3.120 nonbonded pdb=" O LEU A 279 " pdb=" OG SER A 280 " model vdw 2.258 3.040 nonbonded pdb=" O GLY A 114 " pdb=" N LYS A 117 " model vdw 2.278 3.120 nonbonded pdb=" OD1 ASN A 181 " pdb=" OG1 THR A 183 " model vdw 2.304 3.040 ... (remaining 35066 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: 0.390 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.380 Find NCS groups from input model: 0.040 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: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 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 : 0.006 0.103 4444 Z= 0.295 Angle : 0.862 26.323 6060 Z= 0.421 Chirality : 0.045 0.247 671 Planarity : 0.009 0.180 733 Dihedral : 15.326 102.447 1584 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.11 (0.38), residues: 530 helix: 0.55 (0.27), residues: 395 sheet: None (None), residues: 0 loop : -1.79 (0.56), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 193 HIS 0.002 0.001 HIS A 347 PHE 0.016 0.002 PHE A 512 TYR 0.029 0.002 TYR A 60 ARG 0.003 0.001 ARG A 69 Details of bonding type rmsd link_NAG-ASN : bond 0.09780 ( 3) link_NAG-ASN : angle 12.61290 ( 9) hydrogen bonds : bond 0.11080 ( 282) hydrogen bonds : angle 5.80034 ( 837) SS BOND : bond 0.00608 ( 1) SS BOND : angle 2.12729 ( 2) covalent geometry : bond 0.00597 ( 4440) covalent geometry : angle 0.71185 ( 6049) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.417 Fit side-chains REVERT: A 152 TYR cc_start: 0.8218 (t80) cc_final: 0.7910 (t80) REVERT: A 314 ASN cc_start: 0.8805 (t0) cc_final: 0.8596 (t0) REVERT: A 491 ARG cc_start: 0.8383 (mmm160) cc_final: 0.8061 (ttm170) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.1591 time to fit residues: 14.7324 Evaluate side-chains 69 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 44 optimal weight: 0.1980 chunk 40 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 13 optimal weight: 5.9990 chunk 27 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4096 r_free = 0.4096 target = 0.172512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.132778 restraints weight = 4505.748| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.94 r_work: 0.3067 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4444 Z= 0.163 Angle : 0.709 10.102 6060 Z= 0.348 Chirality : 0.048 0.350 671 Planarity : 0.005 0.040 733 Dihedral : 7.799 88.793 666 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.88 % Allowed : 9.51 % Favored : 89.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.51 (0.38), residues: 530 helix: 0.96 (0.27), residues: 397 sheet: None (None), residues: 0 loop : -1.46 (0.55), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 193 HIS 0.002 0.001 HIS A 347 PHE 0.017 0.002 PHE A 385 TYR 0.025 0.002 TYR A 60 ARG 0.004 0.001 ARG A 566 Details of bonding type rmsd link_NAG-ASN : bond 0.00872 ( 3) link_NAG-ASN : angle 4.60457 ( 9) hydrogen bonds : bond 0.05811 ( 282) hydrogen bonds : angle 4.91766 ( 837) SS BOND : bond 0.00668 ( 1) SS BOND : angle 1.75454 ( 2) covalent geometry : bond 0.00361 ( 4440) covalent geometry : angle 0.68677 ( 6049) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.443 Fit side-chains revert: symmetry clash REVERT: A 314 ASN cc_start: 0.8637 (t0) cc_final: 0.8384 (t0) outliers start: 4 outliers final: 3 residues processed: 64 average time/residue: 0.1138 time to fit residues: 10.3330 Evaluate side-chains 62 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 59 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 469 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 22 optimal weight: 0.4980 chunk 17 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 30 optimal weight: 0.2980 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.173694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.134222 restraints weight = 4487.593| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.93 r_work: 0.3090 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4444 Z= 0.149 Angle : 0.657 9.174 6060 Z= 0.320 Chirality : 0.046 0.366 671 Planarity : 0.004 0.040 733 Dihedral : 7.549 87.752 666 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 1.77 % Allowed : 11.95 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.79 (0.38), residues: 530 helix: 1.21 (0.27), residues: 393 sheet: None (None), residues: 0 loop : -1.43 (0.53), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 193 HIS 0.002 0.001 HIS A 347 PHE 0.020 0.001 PHE A 51 TYR 0.026 0.002 TYR A 60 ARG 0.002 0.000 ARG A 566 Details of bonding type rmsd link_NAG-ASN : bond 0.01006 ( 3) link_NAG-ASN : angle 4.07702 ( 9) hydrogen bonds : bond 0.05458 ( 282) hydrogen bonds : angle 4.77024 ( 837) SS BOND : bond 0.00178 ( 1) SS BOND : angle 1.47322 ( 2) covalent geometry : bond 0.00328 ( 4440) covalent geometry : angle 0.63798 ( 6049) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.421 Fit side-chains REVERT: A 314 ASN cc_start: 0.8646 (t0) cc_final: 0.8406 (t0) REVERT: A 345 MET cc_start: 0.7516 (OUTLIER) cc_final: 0.7243 (mtp) outliers start: 8 outliers final: 4 residues processed: 64 average time/residue: 0.1119 time to fit residues: 10.1427 Evaluate side-chains 64 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 469 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 31 optimal weight: 0.2980 chunk 2 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 51 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 26 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4114 r_free = 0.4114 target = 0.174034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.134561 restraints weight = 4500.113| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.93 r_work: 0.3129 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4444 Z= 0.148 Angle : 0.636 8.832 6060 Z= 0.311 Chirality : 0.045 0.362 671 Planarity : 0.004 0.043 733 Dihedral : 7.557 86.184 666 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.21 % Allowed : 13.50 % Favored : 84.29 % 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: 0.93 (0.38), residues: 530 helix: 1.33 (0.27), residues: 393 sheet: None (None), residues: 0 loop : -1.44 (0.53), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 193 HIS 0.001 0.001 HIS A 347 PHE 0.013 0.001 PHE A 51 TYR 0.026 0.001 TYR A 60 ARG 0.002 0.000 ARG A 318 Details of bonding type rmsd link_NAG-ASN : bond 0.01044 ( 3) link_NAG-ASN : angle 4.06189 ( 9) hydrogen bonds : bond 0.05372 ( 282) hydrogen bonds : angle 4.71376 ( 837) SS BOND : bond 0.00196 ( 1) SS BOND : angle 1.18919 ( 2) covalent geometry : bond 0.00330 ( 4440) covalent geometry : angle 0.61688 ( 6049) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.423 Fit side-chains revert: symmetry clash REVERT: A 314 ASN cc_start: 0.8667 (t0) cc_final: 0.8442 (t0) REVERT: A 345 MET cc_start: 0.7569 (OUTLIER) cc_final: 0.7275 (mtp) REVERT: A 355 ASP cc_start: 0.8172 (t0) cc_final: 0.7962 (t0) outliers start: 10 outliers final: 6 residues processed: 74 average time/residue: 0.1134 time to fit residues: 12.1064 Evaluate side-chains 69 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 48 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 19 optimal weight: 0.4980 chunk 52 optimal weight: 0.0270 chunk 28 optimal weight: 0.7980 chunk 6 optimal weight: 0.0770 chunk 22 optimal weight: 0.9980 overall best weight: 0.3996 ------------------------------------------------------------------------------- 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 = 0.4181 r_free = 0.4181 target = 0.183864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.143095 restraints weight = 4734.181| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.05 r_work: 0.2925 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4444 Z= 0.130 Angle : 0.614 8.831 6060 Z= 0.298 Chirality : 0.045 0.364 671 Planarity : 0.004 0.042 733 Dihedral : 7.756 83.397 666 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 1.33 % Allowed : 16.59 % Favored : 82.08 % 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: 0.94 (0.38), residues: 530 helix: 1.23 (0.26), residues: 409 sheet: None (None), residues: 0 loop : -1.39 (0.57), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 193 HIS 0.002 0.001 HIS A 347 PHE 0.014 0.001 PHE A 474 TYR 0.026 0.001 TYR A 60 ARG 0.002 0.000 ARG A 318 Details of bonding type rmsd link_NAG-ASN : bond 0.00972 ( 3) link_NAG-ASN : angle 3.93479 ( 9) hydrogen bonds : bond 0.04861 ( 282) hydrogen bonds : angle 4.62126 ( 837) SS BOND : bond 0.00216 ( 1) SS BOND : angle 1.30767 ( 2) covalent geometry : bond 0.00277 ( 4440) covalent geometry : angle 0.59473 ( 6049) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.455 Fit side-chains REVERT: A 185 MET cc_start: 0.6802 (OUTLIER) cc_final: 0.5939 (mmm) REVERT: A 314 ASN cc_start: 0.8588 (t0) cc_final: 0.8380 (t0) REVERT: A 355 ASP cc_start: 0.8215 (t0) cc_final: 0.7936 (t0) outliers start: 6 outliers final: 5 residues processed: 65 average time/residue: 0.1047 time to fit residues: 9.8237 Evaluate side-chains 64 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 469 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 52 optimal weight: 0.2980 chunk 5 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.175212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.136000 restraints weight = 4488.833| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 1.94 r_work: 0.2911 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4444 Z= 0.142 Angle : 0.622 8.511 6060 Z= 0.304 Chirality : 0.045 0.356 671 Planarity : 0.004 0.044 733 Dihedral : 7.740 82.473 666 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 3.10 % Allowed : 17.04 % Favored : 79.87 % 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: 1.06 (0.38), residues: 530 helix: 1.32 (0.27), residues: 409 sheet: None (None), residues: 0 loop : -1.33 (0.57), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 230 HIS 0.001 0.000 HIS A 347 PHE 0.012 0.001 PHE A 474 TYR 0.027 0.001 TYR A 60 ARG 0.001 0.000 ARG A 318 Details of bonding type rmsd link_NAG-ASN : bond 0.01037 ( 3) link_NAG-ASN : angle 3.79269 ( 9) hydrogen bonds : bond 0.05150 ( 282) hydrogen bonds : angle 4.63488 ( 837) SS BOND : bond 0.00213 ( 1) SS BOND : angle 1.24428 ( 2) covalent geometry : bond 0.00318 ( 4440) covalent geometry : angle 0.60503 ( 6049) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.440 Fit side-chains revert: symmetry clash REVERT: A 185 MET cc_start: 0.6820 (OUTLIER) cc_final: 0.5936 (mmm) REVERT: A 355 ASP cc_start: 0.8285 (t0) cc_final: 0.8044 (t0) outliers start: 14 outliers final: 9 residues processed: 71 average time/residue: 0.1075 time to fit residues: 11.0257 Evaluate side-chains 67 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 327 ASN Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 506 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 40 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 19 optimal weight: 0.3980 chunk 45 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.181103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.140454 restraints weight = 4713.741| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.04 r_work: 0.2877 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4444 Z= 0.148 Angle : 0.633 9.070 6060 Z= 0.309 Chirality : 0.046 0.343 671 Planarity : 0.004 0.044 733 Dihedral : 7.753 83.187 666 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.32 % Allowed : 17.04 % Favored : 79.65 % 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: 1.10 (0.38), residues: 530 helix: 1.34 (0.26), residues: 409 sheet: None (None), residues: 0 loop : -1.27 (0.59), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 230 HIS 0.001 0.000 HIS A 313 PHE 0.011 0.001 PHE A 294 TYR 0.027 0.001 TYR A 60 ARG 0.001 0.000 ARG A 318 Details of bonding type rmsd link_NAG-ASN : bond 0.00837 ( 3) link_NAG-ASN : angle 4.06890 ( 9) hydrogen bonds : bond 0.05296 ( 282) hydrogen bonds : angle 4.64160 ( 837) SS BOND : bond 0.00243 ( 1) SS BOND : angle 1.32438 ( 2) covalent geometry : bond 0.00337 ( 4440) covalent geometry : angle 0.61347 ( 6049) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 55 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: A 179 MET cc_start: 0.6623 (tpt) cc_final: 0.5912 (mmt) REVERT: A 185 MET cc_start: 0.6585 (OUTLIER) cc_final: 0.5900 (mmm) REVERT: A 355 ASP cc_start: 0.8262 (t0) cc_final: 0.8024 (t0) outliers start: 15 outliers final: 10 residues processed: 67 average time/residue: 0.0999 time to fit residues: 9.7382 Evaluate side-chains 66 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 327 ASN Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 506 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 35 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 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 = 0.4112 r_free = 0.4112 target = 0.173361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.133977 restraints weight = 4486.361| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.94 r_work: 0.3082 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4444 Z= 0.154 Angle : 0.636 8.772 6060 Z= 0.312 Chirality : 0.045 0.359 671 Planarity : 0.004 0.045 733 Dihedral : 7.778 83.141 666 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.43 % Allowed : 18.36 % Favored : 79.20 % 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: 1.16 (0.38), residues: 530 helix: 1.37 (0.26), residues: 409 sheet: None (None), residues: 0 loop : -1.23 (0.59), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 230 HIS 0.001 0.000 HIS A 313 PHE 0.011 0.001 PHE A 339 TYR 0.028 0.001 TYR A 60 ARG 0.003 0.000 ARG A 579 Details of bonding type rmsd link_NAG-ASN : bond 0.00851 ( 3) link_NAG-ASN : angle 3.57063 ( 9) hydrogen bonds : bond 0.05443 ( 282) hydrogen bonds : angle 4.66767 ( 837) SS BOND : bond 0.00276 ( 1) SS BOND : angle 1.34179 ( 2) covalent geometry : bond 0.00353 ( 4440) covalent geometry : angle 0.62086 ( 6049) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 250 MET cc_start: 0.7384 (mmm) cc_final: 0.7090 (mmm) REVERT: A 355 ASP cc_start: 0.8347 (t0) cc_final: 0.8119 (t0) REVERT: A 473 TRP cc_start: 0.8793 (m-10) cc_final: 0.8563 (m-10) outliers start: 11 outliers final: 9 residues processed: 66 average time/residue: 0.1083 time to fit residues: 10.3208 Evaluate side-chains 66 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 327 ASN Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 23 optimal weight: 0.8980 chunk 13 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 29 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4127 r_free = 0.4127 target = 0.174707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.135300 restraints weight = 4480.706| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 1.95 r_work: 0.2895 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4444 Z= 0.148 Angle : 0.636 8.651 6060 Z= 0.310 Chirality : 0.046 0.374 671 Planarity : 0.004 0.044 733 Dihedral : 7.814 84.001 666 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.43 % Allowed : 18.58 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.38), residues: 530 helix: 1.39 (0.26), residues: 410 sheet: None (None), residues: 0 loop : -1.14 (0.60), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 230 HIS 0.001 0.000 HIS A 313 PHE 0.010 0.001 PHE A 294 TYR 0.027 0.001 TYR A 60 ARG 0.001 0.000 ARG A 318 Details of bonding type rmsd link_NAG-ASN : bond 0.00902 ( 3) link_NAG-ASN : angle 3.58137 ( 9) hydrogen bonds : bond 0.05269 ( 282) hydrogen bonds : angle 4.62168 ( 837) SS BOND : bond 0.00268 ( 1) SS BOND : angle 1.32738 ( 2) covalent geometry : bond 0.00334 ( 4440) covalent geometry : angle 0.62058 ( 6049) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.451 Fit side-chains revert: symmetry clash REVERT: A 355 ASP cc_start: 0.8342 (t0) cc_final: 0.8090 (t0) REVERT: A 473 TRP cc_start: 0.8748 (m-10) cc_final: 0.8512 (m-10) outliers start: 11 outliers final: 10 residues processed: 65 average time/residue: 0.1134 time to fit residues: 10.5969 Evaluate side-chains 66 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 327 ASN Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 552 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 5 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3501 r_free = 0.3501 target = 0.138384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.098571 restraints weight = 4622.021| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.83 r_work: 0.3084 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 4444 Z= 0.194 Angle : 1.207 57.700 6060 Z= 0.664 Chirality : 0.050 0.620 671 Planarity : 0.004 0.044 733 Dihedral : 7.980 83.564 666 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.43 % Allowed : 18.58 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.38), residues: 530 helix: 1.36 (0.26), residues: 410 sheet: None (None), residues: 0 loop : -1.16 (0.60), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 230 HIS 0.001 0.001 HIS A 313 PHE 0.012 0.001 PHE A 294 TYR 0.027 0.001 TYR A 60 ARG 0.001 0.000 ARG A 318 Details of bonding type rmsd link_NAG-ASN : bond 0.03757 ( 3) link_NAG-ASN : angle 9.98392 ( 9) hydrogen bonds : bond 0.05399 ( 282) hydrogen bonds : angle 4.64094 ( 837) SS BOND : bond 0.00235 ( 1) SS BOND : angle 1.34249 ( 2) covalent geometry : bond 0.00443 ( 4440) covalent geometry : angle 1.14518 ( 6049) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: A 355 ASP cc_start: 0.8406 (t0) cc_final: 0.8160 (t0) REVERT: A 473 TRP cc_start: 0.8790 (m-10) cc_final: 0.8549 (m-10) outliers start: 11 outliers final: 10 residues processed: 65 average time/residue: 0.1059 time to fit residues: 9.9656 Evaluate side-chains 67 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 327 ASN Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 552 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 32 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.3500 r_free = 0.3500 target = 0.138309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.098413 restraints weight = 4633.856| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.83 r_work: 0.3069 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 4444 Z= 0.193 Angle : 1.216 58.171 6060 Z= 0.666 Chirality : 0.048 0.478 671 Planarity : 0.004 0.044 733 Dihedral : 7.936 83.333 666 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.10 % Allowed : 18.14 % Favored : 78.76 % 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: 1.17 (0.38), residues: 530 helix: 1.36 (0.26), residues: 410 sheet: None (None), residues: 0 loop : -1.17 (0.60), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 230 HIS 0.001 0.001 HIS A 313 PHE 0.012 0.001 PHE A 294 TYR 0.027 0.002 TYR A 60 ARG 0.001 0.000 ARG A 69 Details of bonding type rmsd link_NAG-ASN : bond 0.03822 ( 3) link_NAG-ASN : angle 10.47840 ( 9) hydrogen bonds : bond 0.05425 ( 282) hydrogen bonds : angle 4.64728 ( 837) SS BOND : bond 0.00237 ( 1) SS BOND : angle 1.36200 ( 2) covalent geometry : bond 0.00438 ( 4440) covalent geometry : angle 1.14768 ( 6049) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2544.52 seconds wall clock time: 44 minutes 52.02 seconds (2692.02 seconds total)