Starting phenix.real_space_refine on Wed Jul 23 21:29:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y7y_33674/07_2025/7y7y_33674.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y7y_33674/07_2025/7y7y_33674.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y7y_33674/07_2025/7y7y_33674.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y7y_33674/07_2025/7y7y_33674.map" model { file = "/net/cci-nas-00/data/ceres_data/7y7y_33674/07_2025/7y7y_33674.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y7y_33674/07_2025/7y7y_33674.cif" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.109 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: 6 Type Number sf(0) Gaussians S 34 5.16 5 Cl 1 4.86 5 Na 2 4.78 5 C 2838 2.51 5 N 650 2.21 5 O 778 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 4303 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4195 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 22, 'TRANS': 504} Chain: "A" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 108 Unusual residues: {' CL': 1, ' NA': 2, 'ID7': 1, 'NAG': 3} Classifications: {'undetermined': 7, 'water': 54} Link IDs: {None: 60} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.32, per 1000 atoms: 0.77 Number of scatterers: 4303 At special positions: 0 Unit cell: (69.28, 71.445, 95.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 34 16.00 Na 2 11.00 O 778 8.00 N 650 7.00 C 2838 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=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 702 " - " ASN A 181 " " NAG A 703 " - " ASN A 176 " " NAG A 704 " - " ASN A 184 " Time building additional restraints: 1.17 Conformation dependent library (CDL) restraints added in 513.2 milliseconds 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 964 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 2 sheets defined 82.2% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 63 through 68 removed outlier: 3.705A pdb=" N VAL A 67 " --> pdb=" O GLY A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 77 removed outlier: 3.690A pdb=" N TYR A 72 " --> pdb=" O TRP A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 81 No H-bonds generated for 'chain 'A' and resid 79 through 81' Processing helix chain 'A' and resid 82 through 93 Processing helix chain 'A' and resid 93 through 109 Processing helix chain 'A' and resid 112 through 118 removed outlier: 3.985A pdb=" N VAL A 115 " --> pdb=" O GLY A 112 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TRP A 116 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 3.682A 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: 3.950A pdb=" N GLY A 126 " --> pdb=" O PHE A 122 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ILE A 141 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL A 142 " --> pdb=" O ILE A 138 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE A 143 " --> pdb=" O TYR A 139 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE A 144 " --> pdb=" O TYR A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 196 Processing helix chain 'A' and resid 211 through 230 Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 239 through 260 Proline residue: A 247 - end of helix removed outlier: 4.136A pdb=" N THR A 260 " --> pdb=" O PHE A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 273 Processing helix chain 'A' and resid 275 through 280 removed outlier: 3.619A pdb=" N SER A 280 " --> pdb=" O ARG A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 297 removed outlier: 3.886A pdb=" N TRP A 285 " --> pdb=" O ASP A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 309 Processing helix chain 'A' and resid 315 through 350 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: 3.693A pdb=" N TRP A 381 " --> pdb=" O ILE A 377 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP A 395 " --> pdb=" O MET A 391 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N SER A 396 " --> pdb=" O LEU A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 417 Processing helix chain 'A' and resid 419 through 435 Processing helix chain 'A' and resid 436 through 440 removed outlier: 4.162A pdb=" N THR A 440 " --> pdb=" O SER A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 454 removed outlier: 3.937A pdb=" N VAL A 446 " --> pdb=" O GLY A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 473 removed outlier: 3.647A pdb=" N LEU A 460 " --> pdb=" O SER A 456 " (cutoff:3.500A) removed outlier: 3.825A 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: 4.402A pdb=" N LYS A 497 " --> pdb=" O CYS A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 518 Processing helix chain 'A' and resid 530 through 546 Processing helix chain 'A' and resid 546 through 559 Processing helix chain 'A' and resid 562 through 571 Processing sheet with id=AA1, first strand: chain 'A' and resid 173 through 174 Processing sheet with id=AA2, first strand: chain 'A' and resid 523 through 524 287 hydrogen bonds defined for protein. 840 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: 1.17 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 622 1.31 - 1.44: 1351 1.44 - 1.56: 2354 1.56 - 1.69: 0 1.69 - 1.81: 54 Bond restraints: 4381 Sorted by residual: bond pdb=" C SER A 456 " pdb=" O SER A 456 " ideal model delta sigma weight residual 1.235 1.187 0.049 1.26e-02 6.30e+03 1.50e+01 bond pdb=" CA SER A 456 " pdb=" CB SER A 456 " ideal model delta sigma weight residual 1.530 1.471 0.059 1.69e-02 3.50e+03 1.21e+01 bond pdb=" C1 ID7 A 701 " pdb=" O1 ID7 A 701 " ideal model delta sigma weight residual 1.249 1.198 0.051 2.00e-02 2.50e+03 6.40e+00 bond pdb=" C1 ID7 A 701 " pdb=" O2 ID7 A 701 " ideal model delta sigma weight residual 1.248 1.202 0.046 2.00e-02 2.50e+03 5.37e+00 bond pdb=" C ALA A 455 " pdb=" N SER A 456 " ideal model delta sigma weight residual 1.332 1.301 0.031 1.40e-02 5.10e+03 5.04e+00 ... (remaining 4376 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 5856 2.18 - 4.37: 95 4.37 - 6.55: 14 6.55 - 8.73: 2 8.73 - 10.92: 1 Bond angle restraints: 5968 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 109.30 120.22 -10.92 2.00e+00 2.50e-01 2.98e+01 angle pdb=" CA THR A 406 " pdb=" CB THR A 406 " pdb=" CG2 THR A 406 " ideal model delta sigma weight residual 110.50 118.74 -8.24 1.70e+00 3.46e-01 2.35e+01 angle pdb=" CA THR A 406 " pdb=" CB THR A 406 " pdb=" OG1 THR A 406 " ideal model delta sigma weight residual 109.60 115.56 -5.96 1.50e+00 4.44e-01 1.58e+01 angle pdb=" CA ASP A 165 " pdb=" CB ASP A 165 " pdb=" CG ASP A 165 " ideal model delta sigma weight residual 112.60 116.54 -3.94 1.00e+00 1.00e+00 1.55e+01 angle pdb=" CA ALA A 455 " pdb=" C ALA A 455 " pdb=" N SER A 456 " ideal model delta sigma weight residual 116.22 121.73 -5.51 1.44e+00 4.82e-01 1.46e+01 ... (remaining 5963 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.05: 2146 17.05 - 34.11: 272 34.11 - 51.16: 75 51.16 - 68.22: 19 68.22 - 85.27: 6 Dihedral angle restraints: 2518 sinusoidal: 999 harmonic: 1519 Sorted by residual: dihedral pdb=" CA PHE A 502 " pdb=" C PHE A 502 " pdb=" N PHE A 503 " pdb=" CA PHE A 503 " ideal model delta harmonic sigma weight residual -180.00 -159.21 -20.79 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA PHE A 339 " pdb=" C PHE A 339 " pdb=" N SER A 340 " pdb=" CA SER A 340 " ideal model delta harmonic sigma weight residual 180.00 160.97 19.03 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CB CYS A 164 " pdb=" SG CYS A 164 " pdb=" SG CYS A 173 " pdb=" CB CYS A 173 " ideal model delta sinusoidal sigma weight residual -86.00 -54.23 -31.77 1 1.00e+01 1.00e-02 1.44e+01 ... (remaining 2515 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.274: 662 0.274 - 0.548: 3 0.548 - 0.821: 0 0.821 - 1.095: 0 1.095 - 1.369: 1 Chirality restraints: 666 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 1.18 1.37 2.00e-01 2.50e+01 4.68e+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 2.18 0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" C1 NAG A 702 " pdb=" ND2 ASN A 181 " pdb=" C2 NAG A 702 " pdb=" O5 NAG A 702 " both_signs ideal model delta sigma weight residual False -2.40 -2.73 0.33 2.00e-01 2.50e+01 2.65e+00 ... (remaining 663 not shown) Planarity restraints: 725 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 184 " 0.008 2.00e-02 2.50e+03 2.35e-01 6.90e+02 pdb=" CG ASN A 184 " -0.062 2.00e-02 2.50e+03 pdb=" OD1 ASN A 184 " 0.191 2.00e-02 2.50e+03 pdb=" ND2 ASN A 184 " -0.405 2.00e-02 2.50e+03 pdb=" C1 NAG A 704 " 0.267 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 176 " 0.073 2.00e-02 2.50e+03 7.26e-02 6.60e+01 pdb=" CG ASN A 176 " -0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN A 176 " -0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN A 176 " -0.116 2.00e-02 2.50e+03 pdb=" C1 NAG A 703 " 0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 181 " -0.046 2.00e-02 2.50e+03 5.43e-02 3.69e+01 pdb=" CG ASN A 181 " 0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN A 181 " -0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN A 181 " 0.092 2.00e-02 2.50e+03 pdb=" C1 NAG A 702 " -0.062 2.00e-02 2.50e+03 ... (remaining 722 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 31 2.41 - 3.03: 2786 3.03 - 3.66: 6773 3.66 - 4.28: 10892 4.28 - 4.90: 17201 Nonbonded interactions: 37683 Sorted by model distance: nonbonded pdb=" O HOH A 803 " pdb=" O HOH A 822 " model vdw 1.789 3.040 nonbonded pdb=" O HOH A 801 " pdb=" O HOH A 805 " model vdw 1.910 3.040 nonbonded pdb=" OE1 GLU A 101 " pdb=" O HOH A 801 " model vdw 1.973 3.040 nonbonded pdb=" OD1 ASP A 287 " pdb=" O HOH A 802 " model vdw 1.987 3.040 nonbonded pdb=" O ALA A 357 " pdb=" O HOH A 803 " model vdw 2.014 3.040 ... (remaining 37678 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: 0.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 14.890 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:13.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 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 : 0.007 0.271 4385 Z= 0.343 Angle : 0.793 18.529 5979 Z= 0.418 Chirality : 0.072 1.369 666 Planarity : 0.005 0.034 722 Dihedral : 16.872 85.271 1551 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.45 % Allowed : 26.56 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.36), residues: 525 helix: 0.73 (0.26), residues: 382 sheet: None (None), residues: 0 loop : -1.11 (0.53), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 161 HIS 0.005 0.002 HIS A 198 PHE 0.027 0.003 PHE A 398 TYR 0.027 0.002 TYR A 72 ARG 0.004 0.001 ARG A 257 Details of bonding type rmsd link_NAG-ASN : bond 0.16995 ( 3) link_NAG-ASN : angle 7.70618 ( 9) hydrogen bonds : bond 0.13720 ( 287) hydrogen bonds : angle 6.19573 ( 840) SS BOND : bond 0.02058 ( 1) SS BOND : angle 6.40781 ( 2) covalent geometry : bond 0.00541 ( 4381) covalent geometry : angle 0.72532 ( 5968) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 64 time to evaluate : 0.484 Fit side-chains REVERT: A 572 GLN cc_start: 0.7403 (tp40) cc_final: 0.7069 (tt0) outliers start: 2 outliers final: 2 residues processed: 65 average time/residue: 1.4699 time to fit residues: 99.0651 Evaluate side-chains 64 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 487 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 43 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 26 optimal weight: 0.2980 chunk 40 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 24 optimal weight: 0.4980 chunk 30 optimal weight: 0.7980 chunk 47 optimal weight: 0.0970 chunk 14 optimal weight: 1.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN A 198 HIS A 483 ASN A 534 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.121632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.093714 restraints weight = 4208.936| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 1.36 r_work: 0.2819 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4385 Z= 0.140 Angle : 0.583 7.773 5979 Z= 0.305 Chirality : 0.043 0.239 666 Planarity : 0.004 0.033 722 Dihedral : 5.404 50.778 650 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.68 % Allowed : 22.77 % Favored : 74.55 % 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: 1.10 (0.37), residues: 525 helix: 1.31 (0.26), residues: 391 sheet: None (None), residues: 0 loop : -0.91 (0.55), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 161 HIS 0.001 0.001 HIS A 198 PHE 0.029 0.002 PHE A 398 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 0.00367 ( 3) link_NAG-ASN : angle 3.12225 ( 9) hydrogen bonds : bond 0.05541 ( 287) hydrogen bonds : angle 4.70063 ( 840) SS BOND : bond 0.00233 ( 1) SS BOND : angle 1.44790 ( 2) covalent geometry : bond 0.00298 ( 4381) covalent geometry : angle 0.56988 ( 5968) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.497 Fit side-chains REVERT: A 163 GLN cc_start: 0.8578 (mt0) cc_final: 0.8330 (mt0) REVERT: A 348 VAL cc_start: 0.8557 (OUTLIER) cc_final: 0.8313 (t) REVERT: A 419 ARG cc_start: 0.7878 (mtt180) cc_final: 0.7476 (mtt90) REVERT: A 485 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.8023 (tt0) REVERT: A 559 LEU cc_start: 0.7624 (mt) cc_final: 0.7324 (mt) REVERT: A 572 GLN cc_start: 0.7456 (tp40) cc_final: 0.7001 (tt0) outliers start: 12 outliers final: 7 residues processed: 72 average time/residue: 1.0970 time to fit residues: 82.2363 Evaluate side-chains 69 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.429 ------------------------------------------------------------------------------- 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 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 485 GLN Chi-restraints excluded: chain A residue 501 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 32 optimal weight: 0.1980 chunk 8 optimal weight: 0.6980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.117971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.089466 restraints weight = 4192.188| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 1.37 r_work: 0.2753 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2651 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 4385 Z= 0.197 Angle : 0.664 8.890 5979 Z= 0.347 Chirality : 0.047 0.241 666 Planarity : 0.004 0.037 722 Dihedral : 5.447 52.143 647 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.90 % Allowed : 21.88 % Favored : 75.22 % 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: 1.09 (0.37), residues: 525 helix: 1.36 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -1.08 (0.54), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 116 HIS 0.002 0.001 HIS A 198 PHE 0.031 0.003 PHE A 398 TYR 0.023 0.002 TYR A 72 ARG 0.003 0.001 ARG A 211 Details of bonding type rmsd link_NAG-ASN : bond 0.00424 ( 3) link_NAG-ASN : angle 2.37260 ( 9) hydrogen bonds : bond 0.06749 ( 287) hydrogen bonds : angle 4.90281 ( 840) SS BOND : bond 0.00046 ( 1) SS BOND : angle 5.91933 ( 2) covalent geometry : bond 0.00466 ( 4381) covalent geometry : angle 0.64929 ( 5968) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.505 Fit side-chains REVERT: A 163 GLN cc_start: 0.8456 (mt0) cc_final: 0.8176 (mt0) REVERT: A 485 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7991 (tt0) REVERT: A 559 LEU cc_start: 0.7766 (mt) cc_final: 0.7410 (mt) REVERT: A 572 GLN cc_start: 0.7468 (tp40) cc_final: 0.7033 (tt0) outliers start: 13 outliers final: 10 residues processed: 70 average time/residue: 1.0805 time to fit residues: 78.8524 Evaluate side-chains 75 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.466 ------------------------------------------------------------------------------- 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 164 CYS Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 485 GLN Chi-restraints excluded: chain A residue 501 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 49 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 24 optimal weight: 0.5980 chunk 25 optimal weight: 7.9990 chunk 13 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 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 314 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.120526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.092024 restraints weight = 4237.032| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 1.35 r_work: 0.2798 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4385 Z= 0.146 Angle : 0.584 7.361 5979 Z= 0.306 Chirality : 0.044 0.197 666 Planarity : 0.004 0.036 722 Dihedral : 5.211 53.573 647 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.12 % Allowed : 21.88 % Favored : 75.00 % 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 (0.37), residues: 525 helix: 1.47 (0.26), residues: 391 sheet: None (None), residues: 0 loop : -1.05 (0.55), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 116 HIS 0.001 0.000 HIS A 198 PHE 0.030 0.002 PHE A 398 TYR 0.023 0.002 TYR A 72 ARG 0.002 0.000 ARG A 414 Details of bonding type rmsd link_NAG-ASN : bond 0.00380 ( 3) link_NAG-ASN : angle 1.80575 ( 9) hydrogen bonds : bond 0.05728 ( 287) hydrogen bonds : angle 4.67999 ( 840) SS BOND : bond 0.00135 ( 1) SS BOND : angle 4.05847 ( 2) covalent geometry : bond 0.00327 ( 4381) covalent geometry : angle 0.57565 ( 5968) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.472 Fit side-chains REVERT: A 163 GLN cc_start: 0.8349 (mt0) cc_final: 0.8098 (mt0) REVERT: A 172 ARG cc_start: 0.7547 (mtp180) cc_final: 0.7296 (mtp-110) REVERT: A 348 VAL cc_start: 0.8550 (OUTLIER) cc_final: 0.8276 (t) REVERT: A 559 LEU cc_start: 0.7829 (mt) cc_final: 0.7453 (mt) REVERT: A 572 GLN cc_start: 0.7462 (tp40) cc_final: 0.7011 (tt0) outliers start: 14 outliers final: 8 residues processed: 79 average time/residue: 1.2013 time to fit residues: 98.4577 Evaluate side-chains 69 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.424 ------------------------------------------------------------------------------- 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 295 SER Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 501 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 chunk 6 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.119308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.090710 restraints weight = 4229.918| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 1.36 r_work: 0.2782 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4385 Z= 0.163 Angle : 0.608 8.959 5979 Z= 0.318 Chirality : 0.045 0.191 666 Planarity : 0.004 0.037 722 Dihedral : 5.165 53.627 647 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.90 % Allowed : 21.65 % Favored : 75.45 % 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: 1.20 (0.37), residues: 525 helix: 1.48 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -1.14 (0.53), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 116 HIS 0.001 0.000 HIS A 198 PHE 0.030 0.002 PHE A 398 TYR 0.024 0.002 TYR A 72 ARG 0.003 0.000 ARG A 211 Details of bonding type rmsd link_NAG-ASN : bond 0.00347 ( 3) link_NAG-ASN : angle 1.65340 ( 9) hydrogen bonds : bond 0.06120 ( 287) hydrogen bonds : angle 4.75314 ( 840) SS BOND : bond 0.00104 ( 1) SS BOND : angle 3.65763 ( 2) covalent geometry : bond 0.00376 ( 4381) covalent geometry : angle 0.60194 ( 5968) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.516 Fit side-chains REVERT: A 163 GLN cc_start: 0.8374 (mt0) cc_final: 0.8168 (mt0) REVERT: A 172 ARG cc_start: 0.7539 (mtp180) cc_final: 0.7296 (mtp-110) REVERT: A 559 LEU cc_start: 0.7871 (mt) cc_final: 0.7487 (mt) REVERT: A 572 GLN cc_start: 0.7468 (tp40) cc_final: 0.7009 (tt0) outliers start: 13 outliers final: 10 residues processed: 74 average time/residue: 1.5391 time to fit residues: 117.8424 Evaluate side-chains 71 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.759 ------------------------------------------------------------------------------- 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 164 CYS Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 501 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 50 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.118480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.089711 restraints weight = 4218.890| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 1.38 r_work: 0.2771 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 4385 Z= 0.180 Angle : 0.634 9.830 5979 Z= 0.330 Chirality : 0.046 0.190 666 Planarity : 0.004 0.036 722 Dihedral : 5.168 53.822 647 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.35 % Allowed : 20.31 % Favored : 76.34 % 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: 1.12 (0.37), residues: 525 helix: 1.43 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -1.18 (0.53), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 116 HIS 0.002 0.001 HIS A 198 PHE 0.031 0.002 PHE A 398 TYR 0.025 0.002 TYR A 72 ARG 0.003 0.000 ARG A 211 Details of bonding type rmsd link_NAG-ASN : bond 0.00355 ( 3) link_NAG-ASN : angle 1.58506 ( 9) hydrogen bonds : bond 0.06418 ( 287) hydrogen bonds : angle 4.81859 ( 840) SS BOND : bond 0.00138 ( 1) SS BOND : angle 4.01578 ( 2) covalent geometry : bond 0.00422 ( 4381) covalent geometry : angle 0.62739 ( 5968) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.473 Fit side-chains REVERT: A 163 GLN cc_start: 0.8439 (mt0) cc_final: 0.8205 (mt0) REVERT: A 172 ARG cc_start: 0.7585 (mtp180) cc_final: 0.7265 (mtp-110) REVERT: A 559 LEU cc_start: 0.7942 (mt) cc_final: 0.7553 (mt) REVERT: A 572 GLN cc_start: 0.7504 (tp40) cc_final: 0.7047 (tt0) outliers start: 15 outliers final: 13 residues processed: 73 average time/residue: 1.0637 time to fit residues: 80.8938 Evaluate side-chains 73 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.480 ------------------------------------------------------------------------------- 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 164 CYS Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 531 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 12 optimal weight: 0.8980 chunk 30 optimal weight: 0.1980 chunk 45 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.121553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.093231 restraints weight = 4174.830| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 1.34 r_work: 0.2829 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4385 Z= 0.134 Angle : 0.569 9.830 5979 Z= 0.294 Chirality : 0.042 0.187 666 Planarity : 0.004 0.034 722 Dihedral : 4.904 54.472 647 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.68 % Allowed : 20.76 % Favored : 76.56 % 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: 1.35 (0.37), residues: 525 helix: 1.55 (0.26), residues: 393 sheet: None (None), residues: 0 loop : -1.06 (0.54), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 116 HIS 0.001 0.000 HIS A 198 PHE 0.029 0.002 PHE A 398 TYR 0.021 0.002 TYR A 72 ARG 0.001 0.000 ARG A 417 Details of bonding type rmsd link_NAG-ASN : bond 0.00334 ( 3) link_NAG-ASN : angle 1.49215 ( 9) hydrogen bonds : bond 0.05334 ( 287) hydrogen bonds : angle 4.58496 ( 840) SS BOND : bond 0.00046 ( 1) SS BOND : angle 2.88287 ( 2) covalent geometry : bond 0.00293 ( 4381) covalent geometry : angle 0.56406 ( 5968) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.779 Fit side-chains REVERT: A 163 GLN cc_start: 0.8350 (mt0) cc_final: 0.8141 (mt0) REVERT: A 172 ARG cc_start: 0.7544 (mtp180) cc_final: 0.7304 (mtp-110) REVERT: A 348 VAL cc_start: 0.8461 (OUTLIER) cc_final: 0.8208 (t) REVERT: A 559 LEU cc_start: 0.7886 (mt) cc_final: 0.7497 (mt) REVERT: A 572 GLN cc_start: 0.7475 (tp40) cc_final: 0.7048 (tt0) outliers start: 12 outliers final: 9 residues processed: 74 average time/residue: 1.9264 time to fit residues: 149.1658 Evaluate side-chains 72 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.791 ------------------------------------------------------------------------------- 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 183 THR Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 501 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 31 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3324 r_free = 0.3324 target = 0.119500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.090940 restraints weight = 4201.189| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 1.36 r_work: 0.2799 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4385 Z= 0.160 Angle : 0.611 10.720 5979 Z= 0.316 Chirality : 0.044 0.181 666 Planarity : 0.004 0.034 722 Dihedral : 4.965 54.151 647 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.68 % Allowed : 20.54 % Favored : 76.79 % 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: 1.27 (0.37), residues: 525 helix: 1.54 (0.26), residues: 389 sheet: None (None), residues: 0 loop : -1.17 (0.52), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 116 HIS 0.001 0.000 HIS A 198 PHE 0.030 0.002 PHE A 398 TYR 0.024 0.002 TYR A 72 ARG 0.003 0.000 ARG A 211 Details of bonding type rmsd link_NAG-ASN : bond 0.00333 ( 3) link_NAG-ASN : angle 1.43405 ( 9) hydrogen bonds : bond 0.06000 ( 287) hydrogen bonds : angle 4.70993 ( 840) SS BOND : bond 0.00106 ( 1) SS BOND : angle 3.42405 ( 2) covalent geometry : bond 0.00367 ( 4381) covalent geometry : angle 0.60567 ( 5968) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.458 Fit side-chains REVERT: A 163 GLN cc_start: 0.8405 (mt0) cc_final: 0.8194 (mt0) REVERT: A 172 ARG cc_start: 0.7537 (mtp180) cc_final: 0.7220 (mtp-110) REVERT: A 559 LEU cc_start: 0.7935 (mt) cc_final: 0.7541 (mt) REVERT: A 572 GLN cc_start: 0.7491 (tp40) cc_final: 0.7030 (tt0) outliers start: 12 outliers final: 11 residues processed: 71 average time/residue: 2.0072 time to fit residues: 148.5210 Evaluate side-chains 70 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 1.226 ------------------------------------------------------------------------------- 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 164 CYS Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 501 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 13 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3345 r_free = 0.3345 target = 0.121111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.092704 restraints weight = 4251.661| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 1.35 r_work: 0.2820 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4385 Z= 0.140 Angle : 0.586 11.469 5979 Z= 0.301 Chirality : 0.043 0.179 666 Planarity : 0.004 0.034 722 Dihedral : 4.857 54.354 647 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.46 % Allowed : 20.76 % Favored : 76.79 % 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: 1.33 (0.37), residues: 525 helix: 1.56 (0.26), residues: 392 sheet: None (None), residues: 0 loop : -1.12 (0.53), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 116 HIS 0.001 0.000 HIS A 198 PHE 0.029 0.002 PHE A 398 TYR 0.022 0.002 TYR A 72 ARG 0.002 0.000 ARG A 211 Details of bonding type rmsd link_NAG-ASN : bond 0.00331 ( 3) link_NAG-ASN : angle 1.39802 ( 9) hydrogen bonds : bond 0.05503 ( 287) hydrogen bonds : angle 4.61194 ( 840) SS BOND : bond 0.00050 ( 1) SS BOND : angle 3.03867 ( 2) covalent geometry : bond 0.00312 ( 4381) covalent geometry : angle 0.58181 ( 5968) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.456 Fit side-chains REVERT: A 172 ARG cc_start: 0.7570 (mtp180) cc_final: 0.7322 (mtp-110) REVERT: A 348 VAL cc_start: 0.8509 (OUTLIER) cc_final: 0.8250 (t) REVERT: A 559 LEU cc_start: 0.8028 (mt) cc_final: 0.7637 (mt) REVERT: A 572 GLN cc_start: 0.7513 (tp40) cc_final: 0.7050 (tt0) outliers start: 11 outliers final: 10 residues processed: 73 average time/residue: 1.0733 time to fit residues: 81.7279 Evaluate side-chains 71 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.482 ------------------------------------------------------------------------------- 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 164 CYS Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 501 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 39 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 18 optimal weight: 0.0670 chunk 37 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 6 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- 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 = 0.3357 r_free = 0.3357 target = 0.122115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.093818 restraints weight = 4185.075| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 1.34 r_work: 0.2837 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4385 Z= 0.133 Angle : 0.574 11.525 5979 Z= 0.293 Chirality : 0.042 0.174 666 Planarity : 0.004 0.033 722 Dihedral : 4.756 54.381 647 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.46 % Allowed : 20.54 % Favored : 77.01 % 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 (0.37), residues: 525 helix: 1.58 (0.26), residues: 394 sheet: None (None), residues: 0 loop : -0.99 (0.53), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 116 HIS 0.001 0.000 HIS A 198 PHE 0.028 0.002 PHE A 398 TYR 0.022 0.002 TYR A 72 ARG 0.002 0.000 ARG A 417 Details of bonding type rmsd link_NAG-ASN : bond 0.00327 ( 3) link_NAG-ASN : angle 1.33589 ( 9) hydrogen bonds : bond 0.05277 ( 287) hydrogen bonds : angle 4.54441 ( 840) SS BOND : bond 0.00067 ( 1) SS BOND : angle 2.63451 ( 2) covalent geometry : bond 0.00291 ( 4381) covalent geometry : angle 0.56983 ( 5968) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.523 Fit side-chains REVERT: A 172 ARG cc_start: 0.7523 (mtp180) cc_final: 0.7226 (mtp-110) REVERT: A 348 VAL cc_start: 0.8441 (OUTLIER) cc_final: 0.8185 (t) REVERT: A 559 LEU cc_start: 0.7891 (mt) cc_final: 0.7499 (mt) REVERT: A 572 GLN cc_start: 0.7542 (tp40) cc_final: 0.7087 (tt0) outliers start: 11 outliers final: 10 residues processed: 71 average time/residue: 1.1024 time to fit residues: 81.5788 Evaluate side-chains 69 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.494 ------------------------------------------------------------------------------- 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 164 CYS Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 501 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 0 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.3336 r_free = 0.3336 target = 0.120504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.091992 restraints weight = 4267.986| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 1.35 r_work: 0.2812 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 4385 Z= 0.150 Angle : 0.605 12.035 5979 Z= 0.309 Chirality : 0.043 0.174 666 Planarity : 0.004 0.034 722 Dihedral : 4.836 53.996 647 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.68 % Allowed : 20.31 % Favored : 77.01 % 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: 1.35 (0.37), residues: 525 helix: 1.55 (0.26), residues: 392 sheet: None (None), residues: 0 loop : -1.05 (0.53), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 116 HIS 0.001 0.000 HIS A 198 PHE 0.029 0.002 PHE A 398 TYR 0.024 0.002 TYR A 72 ARG 0.002 0.000 ARG A 211 Details of bonding type rmsd link_NAG-ASN : bond 0.00319 ( 3) link_NAG-ASN : angle 1.33989 ( 9) hydrogen bonds : bond 0.05764 ( 287) hydrogen bonds : angle 4.64652 ( 840) SS BOND : bond 0.00052 ( 1) SS BOND : angle 3.12046 ( 2) covalent geometry : bond 0.00341 ( 4381) covalent geometry : angle 0.60019 ( 5968) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4405.61 seconds wall clock time: 79 minutes 5.84 seconds (4745.84 seconds total)