Starting phenix.real_space_refine on Wed Jul 23 21:40:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y7v_33671/07_2025/7y7v_33671.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y7v_33671/07_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_33671/07_2025/7y7v_33671.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y7v_33671/07_2025/7y7v_33671.map" model { file = "/net/cci-nas-00/data/ceres_data/7y7v_33671/07_2025/7y7v_33671.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y7v_33671/07_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-5711/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: 3.17, per 1000 atoms: 0.73 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: 1.10 Conformation dependent library (CDL) restraints added in 481.7 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: 0.42 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: 1.28 Time building geometry restraints manager: 1.20 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: 0.380 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.600 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.420 ------------------------------------------------------------------------------- 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 : 0.439 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: 1.1465 time to fit residues: 82.3467 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 : 0.511 ------------------------------------------------------------------------------- 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: 0.6980 chunk 48 optimal weight: 1.9990 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 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 = 0.3634 r_free = 0.3634 target = 0.131269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.098886 restraints weight = 4179.240| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.46 r_work: 0.3088 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1200 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= 0.139 Angle : 0.618 10.392 6031 Z= 0.312 Chirality : 0.048 0.492 670 Planarity : 0.004 0.026 728 Dihedral : 6.339 59.829 641 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.44 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: 1.22 (0.36), residues: 530 helix: 1.51 (0.26), residues: 385 sheet: None (None), residues: 0 loop : -1.07 (0.48), residues: 145 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 0.017 0.002 PHE A 462 TYR 0.017 0.002 TYR A 72 ARG 0.003 0.000 ARG A 420 Details of bonding type rmsd link_NAG-ASN : bond 0.01471 ( 3) link_NAG-ASN : angle 5.38348 ( 9) hydrogen bonds : bond 0.05391 ( 290) hydrogen bonds : angle 4.90040 ( 852) SS BOND : bond 0.00790 ( 1) SS BOND : angle 3.32813 ( 2) covalent geometry : bond 0.00285 ( 4419) covalent geometry : angle 0.57885 ( 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 : 0.394 Fit side-chains REVERT: A 184 ASN cc_start: 0.5744 (OUTLIER) cc_final: 0.5277 (m110) REVERT: A 380 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8236 (tp) REVERT: A 568 GLN cc_start: 0.7182 (OUTLIER) cc_final: 0.6748 (tp40) outliers start: 19 outliers final: 9 residues processed: 74 average time/residue: 1.1222 time to fit residues: 86.4127 Evaluate side-chains 71 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.496 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 1 optimal weight: 0.4980 chunk 35 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 chunk 22 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3632 r_free = 0.3632 target = 0.131047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.098690 restraints weight = 4156.477| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.46 r_work: 0.3085 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4423 Z= 0.135 Angle : 0.586 8.859 6031 Z= 0.298 Chirality : 0.045 0.360 670 Planarity : 0.004 0.030 728 Dihedral : 6.054 58.930 641 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 4.42 % Allowed : 17.26 % Favored : 78.32 % 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: 1.42 (0.36), residues: 530 helix: 1.67 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -1.09 (0.48), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 116 HIS 0.002 0.001 HIS A 313 PHE 0.018 0.002 PHE A 339 TYR 0.018 0.001 TYR A 72 ARG 0.003 0.000 ARG A 172 Details of bonding type rmsd link_NAG-ASN : bond 0.01388 ( 3) link_NAG-ASN : angle 4.62667 ( 9) hydrogen bonds : bond 0.05311 ( 290) hydrogen bonds : angle 4.76915 ( 852) SS BOND : bond 0.00665 ( 1) SS BOND : angle 3.14948 ( 2) covalent geometry : bond 0.00280 ( 4419) covalent geometry : angle 0.55607 ( 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 78 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 58 time to evaluate : 0.761 Fit side-chains REVERT: A 231 LYS cc_start: 0.4863 (OUTLIER) cc_final: 0.4232 (pptt) REVERT: A 278 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8542 (tmtm) REVERT: A 380 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8239 (tp) REVERT: A 568 GLN cc_start: 0.6956 (OUTLIER) cc_final: 0.6506 (tp40) outliers start: 20 outliers final: 9 residues processed: 75 average time/residue: 1.2479 time to fit residues: 97.5349 Evaluate side-chains 78 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.763 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 26 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 19 optimal weight: 0.0980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3630 r_free = 0.3630 target = 0.130801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.098068 restraints weight = 4215.063| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.47 r_work: 0.3077 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4423 Z= 0.139 Angle : 0.583 7.617 6031 Z= 0.303 Chirality : 0.044 0.326 670 Planarity : 0.004 0.034 728 Dihedral : 5.559 42.602 641 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.76 % Allowed : 16.59 % 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: 1.49 (0.36), residues: 530 helix: 1.69 (0.26), residues: 391 sheet: None (None), residues: 0 loop : -1.03 (0.50), residues: 139 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 0.017 0.002 PHE A 339 TYR 0.019 0.002 TYR A 72 ARG 0.002 0.000 ARG A 172 Details of bonding type rmsd link_NAG-ASN : bond 0.00854 ( 3) link_NAG-ASN : angle 3.60234 ( 9) hydrogen bonds : bond 0.05375 ( 290) hydrogen bonds : angle 4.74473 ( 852) SS BOND : bond 0.00441 ( 1) SS BOND : angle 0.37698 ( 2) covalent geometry : bond 0.00293 ( 4419) covalent geometry : angle 0.56626 ( 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 74 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 57 time to evaluate : 0.483 Fit side-chains REVERT: A 231 LYS cc_start: 0.4947 (OUTLIER) cc_final: 0.4361 (pptt) REVERT: A 278 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8550 (tmtm) REVERT: A 380 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8237 (tp) REVERT: A 568 GLN cc_start: 0.6905 (OUTLIER) cc_final: 0.6524 (tp-100) outliers start: 17 outliers final: 10 residues processed: 71 average time/residue: 1.1816 time to fit residues: 87.2711 Evaluate side-chains 76 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.483 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 52 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.129192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.096268 restraints weight = 4227.808| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.48 r_work: 0.3049 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1383 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= 0.153 Angle : 0.612 9.716 6031 Z= 0.311 Chirality : 0.046 0.273 670 Planarity : 0.004 0.036 728 Dihedral : 5.491 44.587 641 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.98 % Allowed : 16.59 % 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: 1.45 (0.36), residues: 530 helix: 1.67 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -1.00 (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 347 PHE 0.018 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 0.01292 ( 3) link_NAG-ASN : angle 4.00829 ( 9) hydrogen bonds : bond 0.05828 ( 290) hydrogen bonds : angle 4.84077 ( 852) SS BOND : bond 0.00466 ( 1) SS BOND : angle 0.87155 ( 2) covalent geometry : bond 0.00329 ( 4419) covalent geometry : angle 0.59283 ( 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 75 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 57 time to evaluate : 0.626 Fit side-chains REVERT: A 184 ASN cc_start: 0.5608 (OUTLIER) cc_final: 0.4797 (p0) REVERT: A 230 TRP cc_start: 0.5451 (OUTLIER) cc_final: 0.4503 (p-90) REVERT: A 278 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8541 (tmtm) REVERT: A 380 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8275 (tp) REVERT: A 568 GLN cc_start: 0.6818 (OUTLIER) cc_final: 0.6456 (tp40) outliers start: 18 outliers final: 11 residues processed: 72 average time/residue: 1.7396 time to fit residues: 131.6591 Evaluate side-chains 78 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 1.011 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 41 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 1 optimal weight: 0.3980 chunk 21 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3633 r_free = 0.3633 target = 0.131062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.098309 restraints weight = 4248.037| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.47 r_work: 0.3079 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1629 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= 0.132 Angle : 0.575 7.487 6031 Z= 0.293 Chirality : 0.044 0.229 670 Planarity : 0.004 0.036 728 Dihedral : 4.989 47.032 641 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 3.98 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: 1.60 (0.37), residues: 530 helix: 1.77 (0.26), residues: 391 sheet: None (None), residues: 0 loop : -0.97 (0.50), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 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 0.01001 ( 3) link_NAG-ASN : angle 3.86004 ( 9) hydrogen bonds : bond 0.05214 ( 290) hydrogen bonds : angle 4.70846 ( 852) SS BOND : bond 0.00410 ( 1) SS BOND : angle 0.99830 ( 2) covalent geometry : bond 0.00275 ( 4419) covalent geometry : angle 0.55577 ( 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 83 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 65 time to evaluate : 1.213 Fit side-chains REVERT: A 184 ASN cc_start: 0.5797 (OUTLIER) cc_final: 0.5313 (p0) REVERT: A 230 TRP cc_start: 0.5445 (OUTLIER) cc_final: 0.5122 (t60) REVERT: A 231 LYS cc_start: 0.4930 (OUTLIER) cc_final: 0.4600 (pptt) REVERT: A 278 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8540 (tmtm) REVERT: A 380 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8249 (tp) REVERT: A 574 SER cc_start: 0.7286 (t) cc_final: 0.7060 (p) outliers start: 18 outliers final: 10 residues processed: 79 average time/residue: 2.8044 time to fit residues: 228.8246 Evaluate side-chains 78 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.693 ------------------------------------------------------------------------------- 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 184 ASN 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: 4.9990 chunk 35 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 = 0.3599 r_free = 0.3599 target = 0.128317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.095388 restraints weight = 4159.570| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.47 r_work: 0.3035 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4423 Z= 0.172 Angle : 0.618 7.267 6031 Z= 0.321 Chirality : 0.047 0.205 670 Planarity : 0.004 0.036 728 Dihedral : 5.097 48.521 641 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 4.65 % Allowed : 16.59 % 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: 1.38 (0.36), residues: 530 helix: 1.60 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -0.97 (0.50), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 116 HIS 0.003 0.001 HIS A 347 PHE 0.017 0.002 PHE A 339 TYR 0.023 0.002 TYR A 72 ARG 0.002 0.000 ARG A 211 Details of bonding type rmsd link_NAG-ASN : bond 0.00920 ( 3) link_NAG-ASN : angle 3.29250 ( 9) hydrogen bonds : bond 0.06228 ( 290) hydrogen bonds : angle 4.92771 ( 852) SS BOND : bond 0.00648 ( 1) SS BOND : angle 1.21573 ( 2) covalent geometry : bond 0.00383 ( 4419) covalent geometry : angle 0.60482 ( 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 85 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 64 time to evaluate : 0.421 Fit side-chains REVERT: A 184 ASN cc_start: 0.5826 (OUTLIER) cc_final: 0.5305 (p0) REVERT: A 230 TRP cc_start: 0.5610 (OUTLIER) cc_final: 0.5196 (t60) REVERT: A 231 LYS cc_start: 0.5172 (OUTLIER) cc_final: 0.4826 (pptt) REVERT: A 278 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8536 (tmtm) REVERT: A 380 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8305 (tp) REVERT: A 559 LEU cc_start: 0.7314 (OUTLIER) cc_final: 0.6911 (mp) REVERT: A 568 GLN cc_start: 0.7655 (OUTLIER) cc_final: 0.6987 (tp40) REVERT: A 574 SER cc_start: 0.7321 (t) cc_final: 0.7101 (p) outliers start: 21 outliers final: 11 residues processed: 82 average time/residue: 1.2463 time to fit residues: 105.8048 Evaluate side-chains 80 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 62 time to evaluate : 0.479 ------------------------------------------------------------------------------- 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 145 SER Chi-restraints excluded: chain A residue 184 ASN 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 559 LEU 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: 0.9990 chunk 35 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 21 optimal weight: 0.0570 chunk 33 optimal weight: 0.5980 overall best weight: 0.6100 ------------------------------------------------------------------------------- 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 = 0.3630 r_free = 0.3630 target = 0.130770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.098125 restraints weight = 4184.457| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 1.47 r_work: 0.3081 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4423 Z= 0.127 Angle : 0.572 9.102 6031 Z= 0.290 Chirality : 0.043 0.203 670 Planarity : 0.004 0.036 728 Dihedral : 4.925 50.551 641 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.98 % Allowed : 17.48 % 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: 1.61 (0.37), residues: 530 helix: 1.77 (0.26), residues: 391 sheet: None (None), residues: 0 loop : -0.97 (0.51), 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 0.021 0.001 TYR A 246 ARG 0.002 0.000 ARG A 172 Details of bonding type rmsd link_NAG-ASN : bond 0.00811 ( 3) link_NAG-ASN : angle 2.99031 ( 9) hydrogen bonds : bond 0.05129 ( 290) hydrogen bonds : angle 4.73003 ( 852) SS BOND : bond 0.00388 ( 1) SS BOND : angle 0.77028 ( 2) covalent geometry : bond 0.00259 ( 4419) covalent geometry : angle 0.56053 ( 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 81 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.436 Fit side-chains REVERT: A 184 ASN cc_start: 0.5753 (OUTLIER) cc_final: 0.5294 (p0) REVERT: A 230 TRP cc_start: 0.5590 (OUTLIER) cc_final: 0.5322 (t60) REVERT: A 231 LYS cc_start: 0.5198 (OUTLIER) cc_final: 0.4864 (pptt) REVERT: A 278 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8534 (tmtm) REVERT: A 380 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8252 (tp) outliers start: 18 outliers final: 10 residues processed: 79 average time/residue: 1.4147 time to fit residues: 115.8977 Evaluate side-chains 79 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.434 ------------------------------------------------------------------------------- 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 184 ASN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 34 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 36 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 26 optimal weight: 0.0000 chunk 32 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 overall best weight: 0.6184 ------------------------------------------------------------------------------- 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 = 0.3640 r_free = 0.3640 target = 0.131618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.099046 restraints weight = 4209.707| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.47 r_work: 0.3095 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: 0.8518 moved from start: 0.1831 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= 0.125 Angle : 0.561 8.766 6031 Z= 0.285 Chirality : 0.043 0.197 670 Planarity : 0.004 0.035 728 Dihedral : 4.832 52.881 641 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % 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: 1.71 (0.37), residues: 530 helix: 1.83 (0.26), residues: 392 sheet: None (None), residues: 0 loop : -0.88 (0.51), residues: 138 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 0.016 0.001 PHE A 462 TYR 0.020 0.001 TYR A 246 ARG 0.002 0.000 ARG A 172 Details of bonding type rmsd link_NAG-ASN : bond 0.00699 ( 3) link_NAG-ASN : angle 2.57353 ( 9) hydrogen bonds : bond 0.04938 ( 290) hydrogen bonds : angle 4.65662 ( 852) SS BOND : bond 0.00389 ( 1) SS BOND : angle 0.75544 ( 2) covalent geometry : bond 0.00256 ( 4419) covalent geometry : angle 0.55281 ( 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 84 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.438 Fit side-chains revert: symmetry clash REVERT: A 50 ARG cc_start: 0.7259 (mmm160) cc_final: 0.6709 (tpt170) REVERT: A 231 LYS cc_start: 0.5110 (OUTLIER) cc_final: 0.4861 (pptt) REVERT: A 278 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8533 (tmtm) REVERT: A 380 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8206 (tp) REVERT: A 572 GLN cc_start: 0.6809 (tp40) cc_final: 0.6555 (tp-100) outliers start: 18 outliers final: 10 residues processed: 81 average time/residue: 1.2371 time to fit residues: 103.7744 Evaluate side-chains 78 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.486 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 52 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 19 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3615 r_free = 0.3615 target = 0.129677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.096726 restraints weight = 4118.514| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.46 r_work: 0.3055 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4423 Z= 0.164 Angle : 0.638 9.304 6031 Z= 0.328 Chirality : 0.046 0.232 670 Planarity : 0.004 0.036 728 Dihedral : 5.093 34.263 639 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % 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: 1.56 (0.36), residues: 530 helix: 1.71 (0.26), residues: 391 sheet: None (None), residues: 0 loop : -0.87 (0.51), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 116 HIS 0.002 0.001 HIS A 347 PHE 0.017 0.002 PHE A 462 TYR 0.023 0.002 TYR A 246 ARG 0.008 0.001 ARG A 172 Details of bonding type rmsd link_NAG-ASN : bond 0.00996 ( 3) link_NAG-ASN : angle 2.67114 ( 9) hydrogen bonds : bond 0.05869 ( 290) hydrogen bonds : angle 4.84513 ( 852) SS BOND : bond 0.00552 ( 1) SS BOND : angle 1.02310 ( 2) covalent geometry : bond 0.00361 ( 4419) covalent geometry : angle 0.63003 ( 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 71 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.476 Fit side-chains REVERT: A 50 ARG cc_start: 0.7235 (OUTLIER) cc_final: 0.3979 (mmm160) REVERT: A 185 MET cc_start: 0.6001 (mmp) cc_final: 0.4834 (mtm) REVERT: A 278 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8522 (tmtm) REVERT: A 380 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8269 (tp) REVERT: A 572 GLN cc_start: 0.6866 (tp40) cc_final: 0.6591 (tp-100) outliers start: 15 outliers final: 10 residues processed: 68 average time/residue: 1.1950 time to fit residues: 84.5637 Evaluate side-chains 69 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ARG 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: 0.7980 chunk 36 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.3608 r_free = 0.3608 target = 0.129015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.096352 restraints weight = 4170.846| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 1.46 r_work: 0.3047 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4423 Z= 0.166 Angle : 0.636 8.654 6031 Z= 0.329 Chirality : 0.046 0.196 670 Planarity : 0.004 0.037 728 Dihedral : 5.185 37.630 639 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % 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: 1.45 (0.36), residues: 530 helix: 1.62 (0.26), residues: 389 sheet: None (None), residues: 0 loop : -0.87 (0.51), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 116 HIS 0.003 0.001 HIS A 313 PHE 0.018 0.002 PHE A 339 TYR 0.023 0.002 TYR A 246 ARG 0.006 0.001 ARG A 172 Details of bonding type rmsd link_NAG-ASN : bond 0.01402 ( 3) link_NAG-ASN : angle 1.96834 ( 9) hydrogen bonds : bond 0.05930 ( 290) hydrogen bonds : angle 4.89879 ( 852) SS BOND : bond 0.00547 ( 1) SS BOND : angle 1.22870 ( 2) covalent geometry : bond 0.00366 ( 4419) covalent geometry : angle 0.63121 ( 6020) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4771.15 seconds wall clock time: 85 minutes 16.29 seconds (5116.29 seconds total)