Starting phenix.real_space_refine on Sat May 10 00:46:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y7v_33671/05_2025/7y7v_33671.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y7v_33671/05_2025/7y7v_33671.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y7v_33671/05_2025/7y7v_33671.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y7v_33671/05_2025/7y7v_33671.map" model { file = "/net/cci-nas-00/data/ceres_data/7y7v_33671/05_2025/7y7v_33671.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y7v_33671/05_2025/7y7v_33671.cif" } resolution = 2.2 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= -0.001 sd= 0.111 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 34 5.16 5 Cl 1 4.86 5 C 2861 2.51 5 N 659 2.21 5 O 786 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 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: 4341 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4240 Classifications: {'peptide': 532} Link IDs: {'PTRANS': 22, 'TRANS': 509} Chain: "A" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 101 Unusual residues: {' CL': 1, 'NAG': 3} Classifications: {'undetermined': 4, 'water': 58} Link IDs: {None: 61} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.06, per 1000 atoms: 0.70 Number of scatterers: 4341 At special positions: 0 Unit cell: (69.28, 71.445, 97.425, 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 34 16.00 O 786 8.00 N 659 7.00 C 2861 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=2.04 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 701 " - " ASN A 181 " " NAG A 702 " - " ASN A 176 " " NAG A 703 " - " ASN A 184 " Time building additional restraints: 1.15 Conformation dependent library (CDL) restraints added in 487.9 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: 32 helices and 1 sheets defined 82.1% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 46 through 57 Processing helix chain 'A' and resid 63 through 68 removed outlier: 3.531A pdb=" N VAL A 67 " --> pdb=" O GLY A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 77 removed outlier: 3.702A pdb=" N TYR A 72 " --> pdb=" O TRP A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 81 removed outlier: 4.763A pdb=" N ALA A 81 " --> pdb=" O GLY A 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 78 through 81' Processing helix chain 'A' and resid 82 through 93 Processing helix chain 'A' and resid 93 through 109 Processing helix chain 'A' and resid 113 through 118 removed outlier: 3.798A pdb=" N TRP A 116 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS A 117 " --> pdb=" O GLY A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 121 No H-bonds generated for 'chain 'A' and resid 119 through 121' Processing helix chain 'A' and resid 122 through 154 removed outlier: 4.031A pdb=" N GLY A 126 " --> pdb=" O PHE A 122 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE A 141 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL A 142 " --> pdb=" O ILE A 138 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE A 143 " --> pdb=" O TYR A 139 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE A 144 " --> pdb=" O TYR A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'A' and resid 211 through 230 Processing helix chain 'A' and resid 233 through 238 removed outlier: 3.599A pdb=" N THR A 236 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 259 Proline residue: A 247 - end of helix Processing helix chain 'A' and resid 263 through 273 Processing helix chain 'A' and resid 275 through 280 removed outlier: 3.709A pdb=" N SER A 280 " --> pdb=" O ARG A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 297 removed outlier: 3.996A pdb=" N TRP A 285 " --> pdb=" O ASP A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 310 removed outlier: 3.615A pdb=" N TYR A 309 " --> pdb=" O ALA A 305 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASN A 310 " --> pdb=" O LEU A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 350 removed outlier: 3.664A pdb=" N ASP A 319 " --> pdb=" O ASN A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 358 Processing helix chain 'A' and resid 363 through 374 Proline residue: A 369 - end of helix Processing helix chain 'A' and resid 377 through 412 removed outlier: 3.727A 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 436 Processing helix chain 'A' and resid 437 through 439 No H-bonds generated for 'chain 'A' and resid 437 through 439' Processing helix chain 'A' and resid 442 through 454 removed outlier: 3.900A pdb=" N VAL A 446 " --> pdb=" O GLY A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 473 removed outlier: 3.775A pdb=" N ILE A 471 " --> pdb=" O GLU A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 489 Processing helix chain 'A' and resid 493 through 502 removed outlier: 4.262A pdb=" N LYS A 497 " --> pdb=" O CYS A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 519 Processing helix chain 'A' and resid 530 through 546 removed outlier: 4.004A pdb=" N SER A 544 " --> pdb=" O MET A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 559 Processing helix chain 'A' and resid 562 through 572 Processing sheet with id=AA1, first strand: chain 'A' and resid 523 through 524 290 hydrogen bonds defined for protein. 852 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: 1.23 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 717 1.33 - 1.46: 1744 1.46 - 1.59: 1904 1.59 - 1.73: 0 1.73 - 1.86: 54 Bond restraints: 4419 Sorted by residual: bond pdb=" C ARG A 172 " pdb=" O ARG A 172 " ideal model delta sigma weight residual 1.235 1.194 0.042 1.33e-02 5.65e+03 9.84e+00 bond pdb=" C ASP A 171 " pdb=" N ARG A 172 " ideal model delta sigma weight residual 1.331 1.305 0.026 1.43e-02 4.89e+03 3.40e+00 bond pdb=" C1 NAG A 702 " pdb=" O5 NAG A 702 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.16e+00 bond pdb=" C1 NAG A 703 " pdb=" O5 NAG A 703 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.01e+00 bond pdb=" C1 NAG A 701 " pdb=" O5 NAG A 701 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.90e+00 ... (remaining 4414 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 5911 2.26 - 4.52: 96 4.52 - 6.78: 11 6.78 - 9.04: 1 9.04 - 11.30: 1 Bond angle restraints: 6020 Sorted by residual: angle pdb=" OG1 THR A 406 " pdb=" CB THR A 406 " pdb=" CG2 THR A 406 " ideal model delta sigma weight residual 109.30 120.60 -11.30 2.00e+00 2.50e-01 3.19e+01 angle pdb=" CA THR A 406 " pdb=" CB THR A 406 " pdb=" CG2 THR A 406 " ideal model delta sigma weight residual 110.50 118.65 -8.15 1.70e+00 3.46e-01 2.30e+01 angle pdb=" CA THR A 406 " pdb=" CB THR A 406 " pdb=" OG1 THR A 406 " ideal model delta sigma weight residual 109.60 115.67 -6.07 1.50e+00 4.44e-01 1.64e+01 angle pdb=" CA ARG A 172 " pdb=" C ARG A 172 " pdb=" O ARG A 172 " ideal model delta sigma weight residual 119.43 114.55 4.88 1.21e+00 6.83e-01 1.63e+01 angle pdb=" N ASP A 52 " pdb=" CA ASP A 52 " pdb=" C ASP A 52 " ideal model delta sigma weight residual 111.28 115.47 -4.19 1.09e+00 8.42e-01 1.48e+01 ... (remaining 6015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.28: 2160 16.28 - 32.57: 264 32.57 - 48.85: 83 48.85 - 65.14: 19 65.14 - 81.42: 5 Dihedral angle restraints: 2531 sinusoidal: 999 harmonic: 1532 Sorted by residual: dihedral pdb=" CA GLY A 111 " pdb=" C GLY A 111 " pdb=" N GLY A 112 " pdb=" CA GLY A 112 " ideal model delta harmonic sigma weight residual 180.00 -159.61 -20.39 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA GLN A 199 " pdb=" C GLN A 199 " pdb=" N MET A 200 " pdb=" CA MET A 200 " ideal model delta harmonic sigma weight residual 180.00 -159.74 -20.26 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA TYR A 453 " pdb=" C TYR A 453 " pdb=" N SER A 454 " pdb=" CA SER A 454 " ideal model delta harmonic sigma weight residual 180.00 -159.98 -20.02 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 2528 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.283: 667 0.283 - 0.565: 2 0.565 - 0.848: 0 0.848 - 1.131: 0 1.131 - 1.413: 1 Chirality restraints: 670 Sorted by residual: chirality pdb=" CB THR A 406 " pdb=" CA THR A 406 " pdb=" OG1 THR A 406 " pdb=" CG2 THR A 406 " both_signs ideal model delta sigma weight residual False 2.55 1.14 1.41 2.00e-01 2.50e+01 4.99e+01 chirality pdb=" CA ASP A 52 " pdb=" N ASP A 52 " pdb=" C ASP A 52 " pdb=" CB ASP A 52 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.52e+00 chirality pdb=" C1 NAG A 702 " pdb=" ND2 ASN A 176 " pdb=" C2 NAG A 702 " pdb=" O5 NAG A 702 " both_signs ideal model delta sigma weight residual False -2.40 -2.75 0.35 2.00e-01 2.50e+01 3.00e+00 ... (remaining 667 not shown) Planarity restraints: 731 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 184 " 0.157 2.00e-02 2.50e+03 1.65e-01 3.38e+02 pdb=" CG ASN A 184 " -0.059 2.00e-02 2.50e+03 pdb=" OD1 ASN A 184 " -0.059 2.00e-02 2.50e+03 pdb=" ND2 ASN A 184 " -0.246 2.00e-02 2.50e+03 pdb=" C1 NAG A 703 " 0.207 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 181 " -0.031 2.00e-02 2.50e+03 3.38e-02 1.42e+01 pdb=" CG ASN A 181 " 0.011 2.00e-02 2.50e+03 pdb=" OD1 ASN A 181 " 0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN A 181 " 0.055 2.00e-02 2.50e+03 pdb=" C1 NAG A 701 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 176 " 0.024 2.00e-02 2.50e+03 2.51e-02 7.87e+00 pdb=" CG ASN A 176 " -0.006 2.00e-02 2.50e+03 pdb=" OD1 ASN A 176 " -0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN A 176 " -0.038 2.00e-02 2.50e+03 pdb=" C1 NAG A 702 " 0.031 2.00e-02 2.50e+03 ... (remaining 728 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 50 2.64 - 3.21: 4207 3.21 - 3.77: 7211 3.77 - 4.34: 10093 4.34 - 4.90: 15768 Nonbonded interactions: 37329 Sorted by model distance: nonbonded pdb=" O SER A 243 " pdb=" O HOH A 801 " model vdw 2.078 3.040 nonbonded pdb=" OH TYR A 140 " pdb=" O HOH A 802 " model vdw 2.079 3.040 nonbonded pdb=" O MET A 570 " pdb=" O HOH A 803 " model vdw 2.151 3.040 nonbonded pdb=" OD1 ASN A 184 " pdb=" O5 NAG A 703 " model vdw 2.209 3.040 nonbonded pdb=" O LYS A 564 " pdb=" OE1 GLN A 568 " model vdw 2.252 3.040 ... (remaining 37324 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: 0.340 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: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.500 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 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 0.121 4423 Z= 0.259 Angle : 0.782 12.420 6031 Z= 0.417 Chirality : 0.073 1.413 670 Planarity : 0.005 0.033 728 Dihedral : 16.081 81.423 1556 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.11 % Allowed : 22.35 % Favored : 76.55 % 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: 0.09 (0.34), residues: 530 helix: 0.62 (0.25), residues: 382 sheet: None (None), residues: 0 loop : -1.26 (0.47), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 116 HIS 0.002 0.001 HIS A 347 PHE 0.022 0.003 PHE A 339 TYR 0.024 0.002 TYR A 72 ARG 0.007 0.002 ARG A 50 Details of bonding type rmsd link_NAG-ASN : bond 0.09672 ( 3) link_NAG-ASN : angle 7.05430 ( 9) hydrogen bonds : bond 0.13768 ( 290) hydrogen bonds : angle 6.58099 ( 852) SS BOND : bond 0.00695 ( 1) SS BOND : angle 5.97461 ( 2) covalent geometry : bond 0.00497 ( 4419) covalent geometry : angle 0.72606 ( 6020) *********************** 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 70 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.478 Fit side-chains REVERT: A 568 GLN cc_start: 0.7303 (mp10) cc_final: 0.6874 (tp40) outliers start: 5 outliers final: 1 residues processed: 69 average time/residue: 1.1235 time to fit residues: 80.7135 Evaluate side-chains 65 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 64 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 44 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 21 optimal weight: 5.9990 chunk 41 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 30 optimal weight: 0.1980 chunk 48 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN A 418 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.131494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.099135 restraints weight = 4180.508| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.46 r_work: 0.3093 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4423 Z= 0.138 Angle : 0.609 11.042 6031 Z= 0.308 Chirality : 0.047 0.472 670 Planarity : 0.004 0.025 728 Dihedral : 6.208 55.252 641 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 4.20 % Allowed : 18.14 % Favored : 77.65 % 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: 1.24 (0.36), residues: 530 helix: 1.53 (0.26), residues: 385 sheet: None (None), residues: 0 loop : -1.06 (0.48), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 116 HIS 0.001 0.001 HIS A 313 PHE 0.018 0.002 PHE A 462 TYR 0.017 0.001 TYR A 72 ARG 0.003 0.000 ARG A 420 Details of bonding type rmsd link_NAG-ASN : bond 0.01039 ( 3) link_NAG-ASN : angle 5.39533 ( 9) hydrogen bonds : bond 0.05409 ( 290) hydrogen bonds : angle 4.90832 ( 852) SS BOND : bond 0.00672 ( 1) SS BOND : angle 3.41358 ( 2) covalent geometry : bond 0.00277 ( 4419) covalent geometry : angle 0.56940 ( 6020) *********************** 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 79 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 60 time to evaluate : 0.459 Fit side-chains REVERT: A 380 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8224 (tp) REVERT: A 568 GLN cc_start: 0.7205 (OUTLIER) cc_final: 0.6788 (tp40) outliers start: 19 outliers final: 9 residues processed: 74 average time/residue: 1.1167 time to fit residues: 85.9100 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 : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 230 TRP Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 568 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 45 optimal weight: 0.9990 chunk 1 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 19 optimal weight: 9.9990 chunk 22 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 44 optimal weight: 0.0870 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.131798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.099292 restraints weight = 4158.319| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.47 r_work: 0.3096 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4423 Z= 0.130 Angle : 0.593 10.494 6031 Z= 0.297 Chirality : 0.044 0.310 670 Planarity : 0.004 0.029 728 Dihedral : 5.524 40.113 641 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 4.87 % Allowed : 16.59 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.36), residues: 530 helix: 1.67 (0.26), residues: 391 sheet: None (None), residues: 0 loop : -1.00 (0.50), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 116 HIS 0.001 0.001 HIS A 313 PHE 0.017 0.002 PHE A 339 TYR 0.017 0.001 TYR A 72 ARG 0.002 0.000 ARG A 417 Details of bonding type rmsd link_NAG-ASN : bond 0.01256 ( 3) link_NAG-ASN : angle 5.42785 ( 9) hydrogen bonds : bond 0.05144 ( 290) hydrogen bonds : angle 4.73719 ( 852) SS BOND : bond 0.00396 ( 1) SS BOND : angle 2.92494 ( 2) covalent geometry : bond 0.00266 ( 4419) covalent geometry : angle 0.55242 ( 6020) *********************** 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 80 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 58 time to evaluate : 0.436 Fit side-chains REVERT: A 231 LYS cc_start: 0.4841 (OUTLIER) cc_final: 0.4207 (pptt) REVERT: A 278 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8554 (tmtm) REVERT: A 380 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8224 (tp) REVERT: A 559 LEU cc_start: 0.7366 (OUTLIER) cc_final: 0.6976 (mp) REVERT: A 568 GLN cc_start: 0.6960 (OUTLIER) cc_final: 0.6512 (tp40) outliers start: 22 outliers final: 9 residues processed: 75 average time/residue: 1.1709 time to fit residues: 91.2890 Evaluate side-chains 77 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 230 TRP Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 568 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 25 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 26 optimal weight: 0.0570 chunk 28 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 19 optimal weight: 10.0000 overall best weight: 1.1702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.129308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.096534 restraints weight = 4184.124| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.47 r_work: 0.3052 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4423 Z= 0.156 Angle : 0.605 7.522 6031 Z= 0.311 Chirality : 0.046 0.286 670 Planarity : 0.004 0.034 728 Dihedral : 5.519 42.056 641 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 4.42 % Allowed : 16.15 % Favored : 79.42 % 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: 1.40 (0.36), residues: 530 helix: 1.64 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -1.05 (0.49), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 116 HIS 0.002 0.001 HIS A 313 PHE 0.018 0.002 PHE A 339 TYR 0.021 0.002 TYR A 72 ARG 0.002 0.000 ARG A 351 Details of bonding type rmsd link_NAG-ASN : bond 0.00953 ( 3) link_NAG-ASN : angle 3.68240 ( 9) hydrogen bonds : bond 0.05890 ( 290) hydrogen bonds : angle 4.86986 ( 852) SS BOND : bond 0.00614 ( 1) SS BOND : angle 0.25241 ( 2) covalent geometry : bond 0.00340 ( 4419) covalent geometry : angle 0.58906 ( 6020) *********************** 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 78 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 58 time to evaluate : 0.467 Fit side-chains REVERT: A 172 ARG cc_start: 0.7659 (mtp85) cc_final: 0.7312 (mtp85) REVERT: A 184 ASN cc_start: 0.5913 (OUTLIER) cc_final: 0.5367 (m110) REVERT: A 278 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8524 (tmtm) REVERT: A 380 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8258 (tp) REVERT: A 568 GLN cc_start: 0.6947 (OUTLIER) cc_final: 0.6545 (tp-100) outliers start: 20 outliers final: 12 residues processed: 75 average time/residue: 1.0925 time to fit residues: 85.3365 Evaluate side-chains 72 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 230 TRP Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 568 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 52 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 18 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 36 optimal weight: 0.0970 chunk 14 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.130274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.097517 restraints weight = 4248.702| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.48 r_work: 0.3068 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4423 Z= 0.140 Angle : 0.575 7.942 6031 Z= 0.296 Chirality : 0.043 0.226 670 Planarity : 0.004 0.035 728 Dihedral : 5.103 44.690 641 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.98 % Allowed : 16.81 % 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: 1.51 (0.36), residues: 530 helix: 1.69 (0.26), residues: 392 sheet: None (None), residues: 0 loop : -0.99 (0.50), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 116 HIS 0.002 0.001 HIS A 313 PHE 0.018 0.002 PHE A 339 TYR 0.018 0.002 TYR A 72 ARG 0.003 0.000 ARG A 172 Details of bonding type rmsd link_NAG-ASN : bond 0.00873 ( 3) link_NAG-ASN : angle 2.86630 ( 9) hydrogen bonds : bond 0.05454 ( 290) hydrogen bonds : angle 4.74880 ( 852) SS BOND : bond 0.00464 ( 1) SS BOND : angle 0.76885 ( 2) covalent geometry : bond 0.00299 ( 4419) covalent geometry : angle 0.56480 ( 6020) *********************** 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 76 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 0.500 Fit side-chains REVERT: A 230 TRP cc_start: 0.5422 (OUTLIER) cc_final: 0.4990 (t60) REVERT: A 231 LYS cc_start: 0.4837 (OUTLIER) cc_final: 0.4466 (pptt) REVERT: A 278 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8541 (tmtm) REVERT: A 380 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8242 (tp) REVERT: A 568 GLN cc_start: 0.6776 (OUTLIER) cc_final: 0.6418 (tp40) outliers start: 18 outliers final: 9 residues processed: 72 average time/residue: 1.1440 time to fit residues: 85.6524 Evaluate side-chains 70 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 230 TRP Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 568 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 41 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 1 optimal weight: 0.1980 chunk 21 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.131336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.098488 restraints weight = 4243.123| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.48 r_work: 0.3084 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4423 Z= 0.131 Angle : 0.589 9.680 6031 Z= 0.301 Chirality : 0.044 0.290 670 Planarity : 0.004 0.035 728 Dihedral : 5.008 46.895 641 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 4.42 % Allowed : 16.59 % 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: 1.60 (0.37), residues: 530 helix: 1.78 (0.26), residues: 391 sheet: None (None), residues: 0 loop : -1.02 (0.50), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 116 HIS 0.001 0.001 HIS A 313 PHE 0.017 0.002 PHE A 339 TYR 0.018 0.001 TYR A 72 ARG 0.002 0.000 ARG A 172 Details of bonding type rmsd link_NAG-ASN : bond 0.00957 ( 3) link_NAG-ASN : angle 3.13279 ( 9) hydrogen bonds : bond 0.05148 ( 290) hydrogen bonds : angle 4.67540 ( 852) SS BOND : bond 0.00641 ( 1) SS BOND : angle 0.69963 ( 2) covalent geometry : bond 0.00270 ( 4419) covalent geometry : angle 0.57637 ( 6020) *********************** 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 79 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 59 time to evaluate : 0.428 Fit side-chains REVERT: A 230 TRP cc_start: 0.5381 (OUTLIER) cc_final: 0.5071 (t60) REVERT: A 231 LYS cc_start: 0.4898 (OUTLIER) cc_final: 0.4579 (pptt) REVERT: A 278 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8539 (tmtm) REVERT: A 380 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8229 (tp) REVERT: A 574 SER cc_start: 0.7296 (t) cc_final: 0.7060 (p) outliers start: 20 outliers final: 11 residues processed: 76 average time/residue: 1.1272 time to fit residues: 89.0851 Evaluate side-chains 80 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 230 TRP Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 31 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 chunk 3 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN A 418 ASN A 568 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.129443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.096719 restraints weight = 4177.613| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.47 r_work: 0.3057 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4423 Z= 0.149 Angle : 0.599 8.752 6031 Z= 0.306 Chirality : 0.046 0.265 670 Planarity : 0.004 0.036 728 Dihedral : 4.982 48.388 641 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 4.20 % Allowed : 17.04 % 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: 1.52 (0.36), residues: 530 helix: 1.69 (0.26), residues: 392 sheet: None (None), residues: 0 loop : -0.96 (0.51), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 116 HIS 0.002 0.001 HIS A 347 PHE 0.017 0.002 PHE A 339 TYR 0.021 0.002 TYR A 72 ARG 0.002 0.000 ARG A 172 Details of bonding type rmsd link_NAG-ASN : bond 0.00849 ( 3) link_NAG-ASN : angle 2.89404 ( 9) hydrogen bonds : bond 0.05701 ( 290) hydrogen bonds : angle 4.79952 ( 852) SS BOND : bond 0.00482 ( 1) SS BOND : angle 0.85556 ( 2) covalent geometry : bond 0.00323 ( 4419) covalent geometry : angle 0.58905 ( 6020) *********************** 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 77 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 58 time to evaluate : 0.437 Fit side-chains REVERT: A 230 TRP cc_start: 0.5517 (OUTLIER) cc_final: 0.5214 (t60) REVERT: A 231 LYS cc_start: 0.5057 (OUTLIER) cc_final: 0.4654 (pptt) REVERT: A 278 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8527 (tmtm) REVERT: A 380 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8270 (tp) REVERT: A 568 GLN cc_start: 0.7646 (OUTLIER) cc_final: 0.6941 (tp40) REVERT: A 572 GLN cc_start: 0.6817 (tp40) cc_final: 0.6555 (tp-100) REVERT: A 574 SER cc_start: 0.7283 (t) cc_final: 0.7080 (p) outliers start: 19 outliers final: 13 residues processed: 74 average time/residue: 1.0872 time to fit residues: 83.6739 Evaluate side-chains 75 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 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 76 LYS Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 230 TRP Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 568 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 2 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 17 optimal weight: 0.4980 chunk 42 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 21 optimal weight: 0.0980 chunk 33 optimal weight: 0.0770 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 ASN A 568 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.132226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.099838 restraints weight = 4205.028| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.47 r_work: 0.3106 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4423 Z= 0.120 Angle : 0.548 7.822 6031 Z= 0.278 Chirality : 0.043 0.227 670 Planarity : 0.004 0.036 728 Dihedral : 4.781 49.870 641 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.98 % Allowed : 17.26 % 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: 1.73 (0.37), residues: 530 helix: 1.87 (0.26), residues: 391 sheet: None (None), residues: 0 loop : -0.96 (0.50), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 116 HIS 0.001 0.001 HIS A 313 PHE 0.016 0.001 PHE A 462 TYR 0.019 0.001 TYR A 246 ARG 0.003 0.000 ARG A 172 Details of bonding type rmsd link_NAG-ASN : bond 0.00755 ( 3) link_NAG-ASN : angle 2.58366 ( 9) hydrogen bonds : bond 0.04744 ( 290) hydrogen bonds : angle 4.62018 ( 852) SS BOND : bond 0.00353 ( 1) SS BOND : angle 0.73037 ( 2) covalent geometry : bond 0.00239 ( 4419) covalent geometry : angle 0.53869 ( 6020) *********************** 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 77 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 0.435 Fit side-chains revert: symmetry clash REVERT: A 231 LYS cc_start: 0.5168 (OUTLIER) cc_final: 0.4861 (pptt) REVERT: A 278 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8524 (tmtm) REVERT: A 380 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8218 (tp) REVERT: A 572 GLN cc_start: 0.6878 (tp40) cc_final: 0.6614 (tp-100) REVERT: A 574 SER cc_start: 0.7308 (t) cc_final: 0.7095 (p) outliers start: 18 outliers final: 10 residues processed: 74 average time/residue: 1.1230 time to fit residues: 86.3637 Evaluate side-chains 71 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 422 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 34 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 26 optimal weight: 0.0060 chunk 32 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 ASN A 568 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.131936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.099357 restraints weight = 4221.277| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.47 r_work: 0.3096 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4423 Z= 0.125 Angle : 0.552 7.675 6031 Z= 0.282 Chirality : 0.043 0.219 670 Planarity : 0.004 0.034 728 Dihedral : 4.217 16.890 639 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.32 % Allowed : 17.48 % 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: 1.73 (0.37), residues: 530 helix: 1.86 (0.26), residues: 392 sheet: None (None), residues: 0 loop : -0.92 (0.50), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 116 HIS 0.001 0.001 HIS A 313 PHE 0.016 0.001 PHE A 339 TYR 0.019 0.001 TYR A 246 ARG 0.002 0.000 ARG A 172 Details of bonding type rmsd link_NAG-ASN : bond 0.00655 ( 3) link_NAG-ASN : angle 2.24737 ( 9) hydrogen bonds : bond 0.04974 ( 290) hydrogen bonds : angle 4.63409 ( 852) SS BOND : bond 0.00377 ( 1) SS BOND : angle 0.80682 ( 2) covalent geometry : bond 0.00255 ( 4419) covalent geometry : angle 0.54588 ( 6020) *********************** 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 74 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 0.454 Fit side-chains revert: symmetry clash REVERT: A 231 LYS cc_start: 0.5174 (OUTLIER) cc_final: 0.4955 (pptt) REVERT: A 278 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8526 (tmtm) REVERT: A 380 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8222 (tp) REVERT: A 572 GLN cc_start: 0.6870 (tp40) cc_final: 0.6520 (tp-100) REVERT: A 574 SER cc_start: 0.7292 (t) cc_final: 0.7050 (p) outliers start: 15 outliers final: 10 residues processed: 72 average time/residue: 1.1764 time to fit residues: 88.1292 Evaluate side-chains 72 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 26 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 chunk 17 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 30 optimal weight: 0.0470 chunk 28 optimal weight: 0.8980 chunk 19 optimal weight: 0.0570 chunk 23 optimal weight: 2.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 ASN A 568 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.133531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.101141 restraints weight = 4152.091| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.46 r_work: 0.3125 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 4423 Z= 0.116 Angle : 0.537 7.564 6031 Z= 0.274 Chirality : 0.042 0.219 670 Planarity : 0.004 0.035 728 Dihedral : 4.119 16.682 639 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.54 % Allowed : 17.26 % 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: 1.85 (0.37), residues: 530 helix: 1.93 (0.26), residues: 393 sheet: None (None), residues: 0 loop : -0.84 (0.50), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 116 HIS 0.001 0.000 HIS A 313 PHE 0.016 0.001 PHE A 462 TYR 0.018 0.001 TYR A 246 ARG 0.002 0.000 ARG A 172 Details of bonding type rmsd link_NAG-ASN : bond 0.00556 ( 3) link_NAG-ASN : angle 1.92261 ( 9) hydrogen bonds : bond 0.04562 ( 290) hydrogen bonds : angle 4.52621 ( 852) SS BOND : bond 0.00327 ( 1) SS BOND : angle 0.75618 ( 2) covalent geometry : bond 0.00236 ( 4419) covalent geometry : angle 0.53219 ( 6020) ********************** 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 73 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 57 time to evaluate : 0.476 Fit side-chains revert: symmetry clash REVERT: A 50 ARG cc_start: 0.7270 (mmm160) cc_final: 0.6807 (tpt170) REVERT: A 156 THR cc_start: 0.8280 (p) cc_final: 0.8067 (t) REVERT: A 278 LYS cc_start: 0.8814 (OUTLIER) cc_final: 0.8534 (tmtm) REVERT: A 380 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8247 (tp) REVERT: A 572 GLN cc_start: 0.6888 (tp40) cc_final: 0.6525 (tp-100) outliers start: 16 outliers final: 10 residues processed: 70 average time/residue: 1.1022 time to fit residues: 80.3801 Evaluate side-chains 68 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 42 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 52 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 23 optimal weight: 0.3980 chunk 18 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 ASN A 568 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.129464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.096552 restraints weight = 4138.702| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.47 r_work: 0.3057 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4423 Z= 0.154 Angle : 0.589 7.581 6031 Z= 0.305 Chirality : 0.045 0.211 670 Planarity : 0.004 0.034 728 Dihedral : 4.353 17.762 639 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.88 % Allowed : 17.26 % 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: 1.63 (0.37), residues: 530 helix: 1.75 (0.26), residues: 393 sheet: None (None), residues: 0 loop : -0.85 (0.51), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 116 HIS 0.002 0.001 HIS A 347 PHE 0.017 0.002 PHE A 339 TYR 0.022 0.002 TYR A 72 ARG 0.002 0.000 ARG A 172 Details of bonding type rmsd link_NAG-ASN : bond 0.00536 ( 3) link_NAG-ASN : angle 1.79853 ( 9) hydrogen bonds : bond 0.05795 ( 290) hydrogen bonds : angle 4.80856 ( 852) SS BOND : bond 0.00444 ( 1) SS BOND : angle 0.90744 ( 2) covalent geometry : bond 0.00337 ( 4419) covalent geometry : angle 0.58482 ( 6020) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3963.91 seconds wall clock time: 68 minutes 50.96 seconds (4130.96 seconds total)