Starting phenix.real_space_refine on Fri May 9 22:30:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9g5k_51088/05_2025/9g5k_51088.cif Found real_map, /net/cci-nas-00/data/ceres_data/9g5k_51088/05_2025/9g5k_51088.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9g5k_51088/05_2025/9g5k_51088.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9g5k_51088/05_2025/9g5k_51088.map" model { file = "/net/cci-nas-00/data/ceres_data/9g5k_51088/05_2025/9g5k_51088.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9g5k_51088/05_2025/9g5k_51088.cif" } resolution = 2.87 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= 0.054 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: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 2674 2.51 5 N 633 2.21 5 O 713 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 4040 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 991 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 1, 'TRANS': 125} Chain: "A" Number of atoms: 3035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3035 Classifications: {'peptide': 380} Link IDs: {'PTRANS': 13, 'TRANS': 366} Chain breaks: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.73, per 1000 atoms: 0.92 Number of scatterers: 4040 At special positions: 0 Unit cell: (87.15, 80.51, 80.51, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 713 8.00 N 633 7.00 C 2674 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 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 601 " - " ASN A 45 " Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 472.4 milliseconds 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 954 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 3 sheets defined 67.3% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'B' and resid 74 through 76 No H-bonds generated for 'chain 'B' and resid 74 through 76' Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'B' and resid 109 through 113 Processing helix chain 'A' and resid 12 through 28 Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 34 through 40 Processing helix chain 'A' and resid 47 through 54 Processing helix chain 'A' and resid 56 through 77 removed outlier: 4.329A pdb=" N THR A 60 " --> pdb=" O PHE A 56 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N LEU A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Proline residue: A 69 - end of helix Processing helix chain 'A' and resid 79 through 100 Processing helix chain 'A' and resid 102 through 119 removed outlier: 3.694A pdb=" N MET A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 131 removed outlier: 4.182A pdb=" N TYR A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ILE A 127 " --> pdb=" O TYR A 123 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N TYR A 128 " --> pdb=" O TYR A 124 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N SER A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL A 130 " --> pdb=" O TYR A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 134 No H-bonds generated for 'chain 'A' and resid 132 through 134' Processing helix chain 'A' and resid 135 through 164 Processing helix chain 'A' and resid 168 through 188 removed outlier: 3.502A pdb=" N ASN A 173 " --> pdb=" O TYR A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 274 Processing helix chain 'A' and resid 275 through 307 removed outlier: 3.699A pdb=" N TYR A 298 " --> pdb=" O GLN A 294 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N GLN A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N ILE A 301 " --> pdb=" O ASN A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 337 Processing helix chain 'A' and resid 340 through 366 removed outlier: 5.316A pdb=" N GLU A 346 " --> pdb=" O ASP A 342 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N LEU A 347 " --> pdb=" O LEU A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 395 removed outlier: 3.667A pdb=" N ILE A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 425 removed outlier: 3.881A pdb=" N ALA A 404 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU A 405 " --> pdb=" O GLU A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 455 removed outlier: 4.136A pdb=" N PHE A 439 " --> pdb=" O VAL A 435 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N LEU A 440 " --> pdb=" O SER A 436 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL A 441 " --> pdb=" O ILE A 437 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 7 removed outlier: 3.506A pdb=" N THR B 78 " --> pdb=" O ASP B 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 11 through 13 removed outlier: 7.384A pdb=" N TYR B 32 " --> pdb=" O ARG B 52 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ARG B 52 " --> pdb=" O TYR B 32 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N MET B 34 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ALA B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 11 through 13 283 hydrogen bonds defined for protein. 810 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: 1.14 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 878 1.33 - 1.45: 1042 1.45 - 1.57: 2198 1.57 - 1.69: 0 1.69 - 1.81: 34 Bond restraints: 4152 Sorted by residual: bond pdb=" CA GLN B 39 " pdb=" C GLN B 39 " ideal model delta sigma weight residual 1.520 1.476 0.044 1.12e-02 7.97e+03 1.53e+01 bond pdb=" CA ASN A 340 " pdb=" C ASN A 340 " ideal model delta sigma weight residual 1.524 1.475 0.049 1.29e-02 6.01e+03 1.43e+01 bond pdb=" N GLN B 39 " pdb=" CA GLN B 39 " ideal model delta sigma weight residual 1.459 1.425 0.034 1.20e-02 6.94e+03 8.22e+00 bond pdb=" CA ASN A 399 " pdb=" C ASN A 399 " ideal model delta sigma weight residual 1.528 1.489 0.039 1.37e-02 5.33e+03 8.10e+00 bond pdb=" CA PRO B 41 " pdb=" C PRO B 41 " ideal model delta sigma weight residual 1.521 1.491 0.030 1.27e-02 6.20e+03 5.75e+00 ... (remaining 4147 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 5510 1.66 - 3.32: 128 3.32 - 4.98: 20 4.98 - 6.63: 2 6.63 - 8.29: 1 Bond angle restraints: 5661 Sorted by residual: angle pdb=" C GLN B 39 " pdb=" CA GLN B 39 " pdb=" CB GLN B 39 " ideal model delta sigma weight residual 110.24 104.46 5.78 1.46e+00 4.69e-01 1.56e+01 angle pdb=" N TYR A 79 " pdb=" CA TYR A 79 " pdb=" C TYR A 79 " ideal model delta sigma weight residual 110.80 119.09 -8.29 2.13e+00 2.20e-01 1.52e+01 angle pdb=" CA LYS A 80 " pdb=" C LYS A 80 " pdb=" N PRO A 81 " ideal model delta sigma weight residual 120.79 117.90 2.89 9.70e-01 1.06e+00 8.88e+00 angle pdb=" N TRP A 94 " pdb=" CA TRP A 94 " pdb=" C TRP A 94 " ideal model delta sigma weight residual 111.82 115.07 -3.25 1.16e+00 7.43e-01 7.84e+00 angle pdb=" C ALA B 40 " pdb=" N PRO B 41 " pdb=" CA PRO B 41 " ideal model delta sigma weight residual 119.76 116.91 2.85 1.03e+00 9.43e-01 7.68e+00 ... (remaining 5656 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.35: 2095 16.35 - 32.70: 203 32.70 - 49.04: 67 49.04 - 65.39: 14 65.39 - 81.74: 5 Dihedral angle restraints: 2384 sinusoidal: 887 harmonic: 1497 Sorted by residual: dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 96 " pdb=" CB CYS B 96 " ideal model delta sinusoidal sigma weight residual 93.00 59.11 33.89 1 1.00e+01 1.00e-02 1.63e+01 dihedral pdb=" C GLN B 39 " pdb=" N GLN B 39 " pdb=" CA GLN B 39 " pdb=" CB GLN B 39 " ideal model delta harmonic sigma weight residual -122.60 -114.27 -8.33 0 2.50e+00 1.60e-01 1.11e+01 dihedral pdb=" N LEU B 11 " pdb=" CA LEU B 11 " pdb=" CB LEU B 11 " pdb=" CG LEU B 11 " ideal model delta sinusoidal sigma weight residual -60.00 -117.11 57.11 3 1.50e+01 4.44e-03 9.43e+00 ... (remaining 2381 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 537 0.053 - 0.107: 91 0.107 - 0.160: 13 0.160 - 0.213: 2 0.213 - 0.266: 2 Chirality restraints: 645 Sorted by residual: chirality pdb=" C1 NAG A 601 " pdb=" ND2 ASN A 45 " pdb=" C2 NAG A 601 " pdb=" O5 NAG A 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CA TRP A 94 " pdb=" N TRP A 94 " pdb=" C TRP A 94 " pdb=" CB TRP A 94 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA ARG A 78 " pdb=" N ARG A 78 " pdb=" C ARG A 78 " pdb=" CB ARG A 78 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.22e-01 ... (remaining 642 not shown) Planarity restraints: 691 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 601 " -0.112 2.00e-02 2.50e+03 9.32e-02 1.09e+02 pdb=" C7 NAG A 601 " 0.030 2.00e-02 2.50e+03 pdb=" C8 NAG A 601 " -0.083 2.00e-02 2.50e+03 pdb=" N2 NAG A 601 " 0.152 2.00e-02 2.50e+03 pdb=" O7 NAG A 601 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 40 " -0.009 2.00e-02 2.50e+03 1.84e-02 3.39e+00 pdb=" C ALA B 40 " 0.032 2.00e-02 2.50e+03 pdb=" O ALA B 40 " -0.012 2.00e-02 2.50e+03 pdb=" N PRO B 41 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 339 " -0.007 2.00e-02 2.50e+03 1.51e-02 2.27e+00 pdb=" C VAL A 339 " 0.026 2.00e-02 2.50e+03 pdb=" O VAL A 339 " -0.010 2.00e-02 2.50e+03 pdb=" N ASN A 340 " -0.009 2.00e-02 2.50e+03 ... (remaining 688 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1033 2.79 - 3.32: 3914 3.32 - 3.85: 6972 3.85 - 4.37: 8161 4.37 - 4.90: 14160 Nonbonded interactions: 34240 Sorted by model distance: nonbonded pdb=" O MET A 384 " pdb=" OG1 THR A 388 " model vdw 2.263 3.040 nonbonded pdb=" O LEU A 415 " pdb=" OG1 THR A 419 " model vdw 2.287 3.040 nonbonded pdb=" O LEU A 177 " pdb=" OG SER A 181 " model vdw 2.312 3.040 nonbonded pdb=" OH TYR A 61 " pdb=" OD2 ASP A 427 " model vdw 2.333 3.040 nonbonded pdb=" O TRP A 12 " pdb=" OG1 THR A 16 " model vdw 2.367 3.040 ... (remaining 34235 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 4.010 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.600 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 4154 Z= 0.286 Angle : 0.616 8.292 5666 Z= 0.365 Chirality : 0.043 0.266 645 Planarity : 0.005 0.093 690 Dihedral : 15.279 81.741 1427 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.70 % Allowed : 15.96 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.37), residues: 501 helix: 1.97 (0.30), residues: 294 sheet: -0.23 (0.60), residues: 53 loop : 0.15 (0.52), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 94 HIS 0.001 0.000 HIS A 364 PHE 0.008 0.001 PHE A 279 TYR 0.011 0.001 TYR A 280 ARG 0.002 0.000 ARG A 78 Details of bonding type rmsd link_NAG-ASN : bond 0.02143 ( 1) link_NAG-ASN : angle 4.99903 ( 3) hydrogen bonds : bond 0.17004 ( 277) hydrogen bonds : angle 6.76142 ( 810) SS BOND : bond 0.00107 ( 1) SS BOND : angle 0.18964 ( 2) covalent geometry : bond 0.00429 ( 4152) covalent geometry : angle 0.60497 ( 5661) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 79 time to evaluate : 0.457 Fit side-chains REVERT: B 89 GLU cc_start: 0.7018 (OUTLIER) cc_final: 0.6769 (mp0) outliers start: 3 outliers final: 1 residues processed: 81 average time/residue: 1.1249 time to fit residues: 94.4299 Evaluate side-chains 74 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 72 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain A residue 449 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 12 optimal weight: 0.4980 chunk 25 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.158338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.142209 restraints weight = 4923.262| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.27 r_work: 0.3429 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4154 Z= 0.184 Angle : 0.626 8.954 5666 Z= 0.326 Chirality : 0.043 0.159 645 Planarity : 0.004 0.034 690 Dihedral : 5.481 56.805 587 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.99 % Allowed : 14.32 % Favored : 81.69 % 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: 1.93 (0.37), residues: 501 helix: 2.12 (0.29), residues: 298 sheet: -0.14 (0.59), residues: 59 loop : 0.23 (0.54), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 94 HIS 0.001 0.001 HIS A 364 PHE 0.015 0.002 PHE A 279 TYR 0.018 0.002 TYR B 113 ARG 0.004 0.000 ARG A 402 Details of bonding type rmsd link_NAG-ASN : bond 0.00075 ( 1) link_NAG-ASN : angle 1.00608 ( 3) hydrogen bonds : bond 0.05292 ( 277) hydrogen bonds : angle 4.55310 ( 810) SS BOND : bond 0.00252 ( 1) SS BOND : angle 0.71688 ( 2) covalent geometry : bond 0.00431 ( 4152) covalent geometry : angle 0.62571 ( 5661) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 0.438 Fit side-chains REVERT: A 78 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.5806 (mpt-90) REVERT: A 349 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.6960 (tp) outliers start: 17 outliers final: 5 residues processed: 87 average time/residue: 1.1038 time to fit residues: 99.5633 Evaluate side-chains 75 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 387 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 GLN A 356 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.159482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.144120 restraints weight = 4906.196| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 1.20 r_work: 0.3420 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 4154 Z= 0.193 Angle : 0.613 8.619 5666 Z= 0.323 Chirality : 0.043 0.153 645 Planarity : 0.004 0.032 690 Dihedral : 4.713 21.061 582 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.69 % Allowed : 16.20 % Favored : 79.11 % 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: 1.88 (0.37), residues: 501 helix: 2.03 (0.29), residues: 301 sheet: -0.06 (0.58), residues: 59 loop : 0.26 (0.53), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 94 HIS 0.002 0.001 HIS A 135 PHE 0.014 0.002 PHE A 439 TYR 0.017 0.002 TYR B 113 ARG 0.004 0.000 ARG A 402 Details of bonding type rmsd link_NAG-ASN : bond 0.00032 ( 1) link_NAG-ASN : angle 0.95776 ( 3) hydrogen bonds : bond 0.05222 ( 277) hydrogen bonds : angle 4.40964 ( 810) SS BOND : bond 0.00266 ( 1) SS BOND : angle 0.52762 ( 2) covalent geometry : bond 0.00454 ( 4152) covalent geometry : angle 0.61261 ( 5661) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 75 time to evaluate : 0.401 Fit side-chains REVERT: B 19 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7115 (ttm-80) REVERT: A 278 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.7166 (tt) outliers start: 20 outliers final: 9 residues processed: 86 average time/residue: 1.0076 time to fit residues: 90.1468 Evaluate side-chains 82 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 449 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 28 optimal weight: 1.9990 chunk 16 optimal weight: 0.4980 chunk 1 optimal weight: 0.5980 chunk 5 optimal weight: 0.0770 chunk 49 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN A 310 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.156274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.141766 restraints weight = 4869.662| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 1.15 r_work: 0.3433 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4154 Z= 0.162 Angle : 0.580 8.257 5666 Z= 0.305 Chirality : 0.042 0.152 645 Planarity : 0.004 0.026 690 Dihedral : 4.665 22.976 582 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.23 % Allowed : 16.67 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.37), residues: 501 helix: 2.12 (0.29), residues: 300 sheet: 0.09 (0.58), residues: 59 loop : 0.34 (0.54), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 94 HIS 0.001 0.001 HIS A 200 PHE 0.014 0.002 PHE A 279 TYR 0.017 0.002 TYR A 280 ARG 0.002 0.000 ARG A 402 Details of bonding type rmsd link_NAG-ASN : bond 0.00098 ( 1) link_NAG-ASN : angle 0.92752 ( 3) hydrogen bonds : bond 0.04763 ( 277) hydrogen bonds : angle 4.27213 ( 810) SS BOND : bond 0.00182 ( 1) SS BOND : angle 0.57466 ( 2) covalent geometry : bond 0.00374 ( 4152) covalent geometry : angle 0.57928 ( 5661) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.408 Fit side-chains REVERT: B 19 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.7066 (ttm-80) REVERT: B 89 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.7158 (mp0) REVERT: A 78 ARG cc_start: 0.7884 (OUTLIER) cc_final: 0.7320 (mtt-85) REVERT: A 278 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7214 (tt) outliers start: 18 outliers final: 8 residues processed: 83 average time/residue: 1.1169 time to fit residues: 96.1049 Evaluate side-chains 80 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 449 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 0.6980 chunk 4 optimal weight: 0.4980 chunk 9 optimal weight: 0.8980 chunk 6 optimal weight: 0.0070 chunk 44 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 40 optimal weight: 0.1980 chunk 30 optimal weight: 0.7980 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN A 297 ASN A 356 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.156755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.142044 restraints weight = 5023.708| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.17 r_work: 0.3437 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4154 Z= 0.148 Angle : 0.571 8.485 5666 Z= 0.300 Chirality : 0.041 0.149 645 Planarity : 0.004 0.027 690 Dihedral : 4.577 22.114 582 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 4.23 % Allowed : 16.90 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.37), residues: 501 helix: 2.15 (0.29), residues: 300 sheet: 0.25 (0.59), residues: 59 loop : 0.41 (0.55), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 94 HIS 0.001 0.001 HIS A 200 PHE 0.011 0.002 PHE A 439 TYR 0.019 0.002 TYR A 280 ARG 0.003 0.000 ARG A 402 Details of bonding type rmsd link_NAG-ASN : bond 0.00068 ( 1) link_NAG-ASN : angle 0.93750 ( 3) hydrogen bonds : bond 0.04595 ( 277) hydrogen bonds : angle 4.18348 ( 810) SS BOND : bond 0.00159 ( 1) SS BOND : angle 0.49972 ( 2) covalent geometry : bond 0.00335 ( 4152) covalent geometry : angle 0.57050 ( 5661) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.409 Fit side-chains REVERT: B 19 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.7025 (ttm-80) REVERT: B 89 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.7157 (mp0) REVERT: A 278 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7136 (tt) outliers start: 18 outliers final: 9 residues processed: 89 average time/residue: 1.0257 time to fit residues: 94.8424 Evaluate side-chains 80 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 449 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 8 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 16 optimal weight: 0.4980 chunk 47 optimal weight: 0.0470 chunk 39 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 46 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN A 297 ASN A 310 GLN A 356 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.157241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.141546 restraints weight = 4891.893| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 1.21 r_work: 0.3433 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4154 Z= 0.152 Angle : 0.576 8.600 5666 Z= 0.302 Chirality : 0.042 0.151 645 Planarity : 0.004 0.026 690 Dihedral : 4.593 21.363 582 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 4.93 % Allowed : 16.20 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.37), residues: 501 helix: 2.15 (0.29), residues: 300 sheet: 0.35 (0.59), residues: 59 loop : 0.41 (0.54), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 94 HIS 0.001 0.001 HIS A 135 PHE 0.019 0.002 PHE A 279 TYR 0.019 0.002 TYR A 280 ARG 0.003 0.000 ARG A 402 Details of bonding type rmsd link_NAG-ASN : bond 0.00072 ( 1) link_NAG-ASN : angle 0.96567 ( 3) hydrogen bonds : bond 0.04582 ( 277) hydrogen bonds : angle 4.16584 ( 810) SS BOND : bond 0.00153 ( 1) SS BOND : angle 0.52736 ( 2) covalent geometry : bond 0.00346 ( 4152) covalent geometry : angle 0.57583 ( 5661) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 75 time to evaluate : 0.416 Fit side-chains REVERT: B 19 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7062 (ttm-80) REVERT: B 89 GLU cc_start: 0.7293 (OUTLIER) cc_final: 0.7083 (mp0) REVERT: A 78 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7451 (mtt-85) REVERT: A 278 LEU cc_start: 0.7590 (OUTLIER) cc_final: 0.7110 (tt) REVERT: A 440 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8238 (tp) outliers start: 21 outliers final: 9 residues processed: 85 average time/residue: 1.0670 time to fit residues: 94.3336 Evaluate side-chains 85 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 449 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 8 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 29 optimal weight: 0.0670 chunk 0 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 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 101 GLN A 297 ASN A 310 GLN A 356 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.155391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.139599 restraints weight = 4928.461| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.22 r_work: 0.3425 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4154 Z= 0.183 Angle : 0.618 9.249 5666 Z= 0.323 Chirality : 0.043 0.154 645 Planarity : 0.004 0.026 690 Dihedral : 4.849 23.624 582 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.93 % Allowed : 16.20 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.37), residues: 501 helix: 1.98 (0.29), residues: 300 sheet: 0.25 (0.59), residues: 59 loop : 0.41 (0.54), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 94 HIS 0.001 0.001 HIS A 200 PHE 0.014 0.002 PHE A 439 TYR 0.019 0.002 TYR A 280 ARG 0.003 0.000 ARG A 402 Details of bonding type rmsd link_NAG-ASN : bond 0.00065 ( 1) link_NAG-ASN : angle 1.01901 ( 3) hydrogen bonds : bond 0.04923 ( 277) hydrogen bonds : angle 4.27362 ( 810) SS BOND : bond 0.00239 ( 1) SS BOND : angle 0.48314 ( 2) covalent geometry : bond 0.00432 ( 4152) covalent geometry : angle 0.61793 ( 5661) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 74 time to evaluate : 0.401 Fit side-chains REVERT: B 19 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7044 (ttm-80) REVERT: B 89 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.7144 (mp0) REVERT: A 78 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.7562 (mpt180) REVERT: A 278 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7197 (tt) REVERT: A 440 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8256 (tp) REVERT: A 459 TYR cc_start: 0.3924 (OUTLIER) cc_final: 0.3179 (m-10) outliers start: 21 outliers final: 9 residues processed: 86 average time/residue: 1.0697 time to fit residues: 95.5561 Evaluate side-chains 86 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 459 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 44 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 5 optimal weight: 0.3980 chunk 24 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 21 optimal weight: 0.0370 chunk 16 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 20 optimal weight: 0.1980 chunk 23 optimal weight: 0.6980 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN A 297 ASN A 310 GLN A 356 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.158367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.142716 restraints weight = 4854.192| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 1.21 r_work: 0.3471 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4154 Z= 0.144 Angle : 0.574 9.340 5666 Z= 0.300 Chirality : 0.041 0.148 645 Planarity : 0.004 0.026 690 Dihedral : 4.583 21.485 582 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.93 % Allowed : 17.14 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.37), residues: 501 helix: 2.17 (0.29), residues: 300 sheet: 0.41 (0.59), residues: 59 loop : 0.42 (0.53), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 94 HIS 0.001 0.000 HIS A 200 PHE 0.024 0.002 PHE A 279 TYR 0.019 0.002 TYR A 280 ARG 0.002 0.000 ARG A 402 Details of bonding type rmsd link_NAG-ASN : bond 0.00131 ( 1) link_NAG-ASN : angle 0.92155 ( 3) hydrogen bonds : bond 0.04445 ( 277) hydrogen bonds : angle 4.10634 ( 810) SS BOND : bond 0.00084 ( 1) SS BOND : angle 0.54636 ( 2) covalent geometry : bond 0.00325 ( 4152) covalent geometry : angle 0.57422 ( 5661) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 74 time to evaluate : 0.392 Fit side-chains REVERT: B 19 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.6957 (ttm-80) REVERT: A 78 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.7376 (mtt-85) REVERT: A 278 LEU cc_start: 0.7590 (OUTLIER) cc_final: 0.7131 (tt) REVERT: A 459 TYR cc_start: 0.3646 (OUTLIER) cc_final: 0.2911 (m-10) outliers start: 21 outliers final: 10 residues processed: 84 average time/residue: 1.0383 time to fit residues: 90.7894 Evaluate side-chains 85 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 459 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 31 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 5 optimal weight: 0.3980 chunk 36 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 27 optimal weight: 0.2980 chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN A 297 ASN A 310 GLN A 356 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.157629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.141133 restraints weight = 4907.474| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 1.30 r_work: 0.3415 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4154 Z= 0.175 Angle : 0.610 9.500 5666 Z= 0.318 Chirality : 0.042 0.153 645 Planarity : 0.004 0.026 690 Dihedral : 4.733 22.610 582 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 4.69 % Allowed : 17.37 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.37), residues: 501 helix: 2.04 (0.29), residues: 300 sheet: 0.35 (0.59), residues: 59 loop : 0.38 (0.54), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 94 HIS 0.001 0.001 HIS A 135 PHE 0.014 0.002 PHE A 439 TYR 0.019 0.002 TYR A 280 ARG 0.002 0.000 ARG A 402 Details of bonding type rmsd link_NAG-ASN : bond 0.00073 ( 1) link_NAG-ASN : angle 0.96125 ( 3) hydrogen bonds : bond 0.04800 ( 277) hydrogen bonds : angle 4.20834 ( 810) SS BOND : bond 0.00195 ( 1) SS BOND : angle 0.49335 ( 2) covalent geometry : bond 0.00412 ( 4152) covalent geometry : angle 0.61009 ( 5661) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 72 time to evaluate : 0.448 Fit side-chains REVERT: B 19 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7013 (ttm-80) REVERT: B 89 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.7073 (mp0) REVERT: A 78 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7507 (mtt-85) REVERT: A 278 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.7202 (tt) REVERT: A 459 TYR cc_start: 0.3968 (OUTLIER) cc_final: 0.3204 (m-10) outliers start: 20 outliers final: 10 residues processed: 83 average time/residue: 1.0268 time to fit residues: 88.5291 Evaluate side-chains 85 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 459 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 5 optimal weight: 0.4980 chunk 6 optimal weight: 0.0170 chunk 38 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 37 optimal weight: 0.0980 chunk 44 optimal weight: 0.6980 overall best weight: 0.3818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN A 297 ASN A 310 GLN A 356 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.158962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.142509 restraints weight = 4881.059| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.31 r_work: 0.3433 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4154 Z= 0.143 Angle : 0.577 9.551 5666 Z= 0.300 Chirality : 0.041 0.148 645 Planarity : 0.004 0.025 690 Dihedral : 4.528 19.853 582 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 4.46 % Allowed : 18.08 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.37), residues: 501 helix: 2.16 (0.29), residues: 300 sheet: 0.47 (0.59), residues: 59 loop : 0.41 (0.53), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 94 HIS 0.001 0.000 HIS A 200 PHE 0.029 0.002 PHE A 279 TYR 0.020 0.002 TYR A 280 ARG 0.002 0.000 ARG A 402 Details of bonding type rmsd link_NAG-ASN : bond 0.00132 ( 1) link_NAG-ASN : angle 0.90729 ( 3) hydrogen bonds : bond 0.04416 ( 277) hydrogen bonds : angle 4.09827 ( 810) SS BOND : bond 0.00092 ( 1) SS BOND : angle 0.51397 ( 2) covalent geometry : bond 0.00325 ( 4152) covalent geometry : angle 0.57694 ( 5661) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 0.436 Fit side-chains REVERT: B 19 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7022 (ttm-80) REVERT: A 78 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7372 (mtt-85) REVERT: A 459 TYR cc_start: 0.3788 (OUTLIER) cc_final: 0.3126 (m-10) outliers start: 19 outliers final: 9 residues processed: 85 average time/residue: 1.0402 time to fit residues: 91.8867 Evaluate side-chains 85 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 459 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 45 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 11 optimal weight: 0.1980 chunk 41 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 5 optimal weight: 0.2980 chunk 3 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN A 297 ASN A 356 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.157077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.142160 restraints weight = 4830.070| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.19 r_work: 0.3437 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4154 Z= 0.162 Angle : 0.612 9.561 5666 Z= 0.317 Chirality : 0.042 0.153 645 Planarity : 0.004 0.026 690 Dihedral : 4.593 20.469 582 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.29 % Allowed : 18.78 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.37), residues: 501 helix: 2.09 (0.29), residues: 299 sheet: 0.41 (0.57), residues: 57 loop : 0.40 (0.54), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 94 HIS 0.001 0.001 HIS A 135 PHE 0.012 0.002 PHE A 439 TYR 0.020 0.002 TYR A 280 ARG 0.002 0.000 ARG A 402 Details of bonding type rmsd link_NAG-ASN : bond 0.00062 ( 1) link_NAG-ASN : angle 0.80358 ( 3) hydrogen bonds : bond 0.04589 ( 277) hydrogen bonds : angle 4.15358 ( 810) SS BOND : bond 0.00163 ( 1) SS BOND : angle 0.51562 ( 2) covalent geometry : bond 0.00377 ( 4152) covalent geometry : angle 0.61189 ( 5661) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3428.97 seconds wall clock time: 60 minutes 12.56 seconds (3612.56 seconds total)