Starting phenix.real_space_refine on Fri May 9 17:32:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y6l_33643/05_2025/7y6l_33643.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y6l_33643/05_2025/7y6l_33643.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y6l_33643/05_2025/7y6l_33643.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y6l_33643/05_2025/7y6l_33643.map" model { file = "/net/cci-nas-00/data/ceres_data/7y6l_33643/05_2025/7y6l_33643.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y6l_33643/05_2025/7y6l_33643.cif" } resolution = 3.5 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= 0.008 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 16 5.16 5 C 2115 2.51 5 N 556 2.21 5 O 621 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 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: 3308 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1519 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 11, 'TRANS': 182} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 17 Chain: "H" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 953 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "L" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 822 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} 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: 2.52, per 1000 atoms: 0.76 Number of scatterers: 3308 At special positions: 0 Unit cell: (101.967, 72.952, 66.32, 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 16 16.00 O 621 8.00 N 556 7.00 C 2115 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 343 " Time building additional restraints: 0.75 Conformation dependent library (CDL) restraints added in 394.4 milliseconds 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 774 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 7 sheets defined 8.5% alpha, 31.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.140A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.722A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 6 removed outlier: 4.063A pdb=" N LEU H 18 " --> pdb=" O TRP H 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 10 through 12 removed outlier: 4.324A pdb=" N TRP H 33 " --> pdb=" O ILE H 99 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ILE H 34 " --> pdb=" O ILE H 50 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ILE H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP H 57 " --> pdb=" O HIS H 52 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.795A pdb=" N CYS H 96 " --> pdb=" O TRP H 112 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N TRP H 112 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ARG H 98 " --> pdb=" O HIS H 110 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA7, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.450A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) 113 hydrogen bonds defined for protein. 261 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: 0.78 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1037 1.35 - 1.48: 969 1.48 - 1.60: 1371 1.60 - 1.73: 0 1.73 - 1.85: 20 Bond restraints: 3397 Sorted by residual: bond pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " ideal model delta sigma weight residual 1.808 1.850 -0.042 3.30e-02 9.18e+02 1.65e+00 bond pdb=" CB VAL A 350 " pdb=" CG1 VAL A 350 " ideal model delta sigma weight residual 1.521 1.483 0.038 3.30e-02 9.18e+02 1.34e+00 bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.429 -0.023 2.00e-02 2.50e+03 1.34e+00 bond pdb=" C5 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.12e+00 bond pdb=" C3 NAG A1301 " pdb=" O3 NAG A1301 " ideal model delta sigma weight residual 1.403 1.423 -0.020 2.00e-02 2.50e+03 9.63e-01 ... (remaining 3392 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 4543 1.74 - 3.48: 67 3.48 - 5.22: 5 5.22 - 6.97: 2 6.97 - 8.71: 1 Bond angle restraints: 4618 Sorted by residual: angle pdb=" CA CYS A 432 " pdb=" CB CYS A 432 " pdb=" SG CYS A 432 " ideal model delta sigma weight residual 114.40 123.11 -8.71 2.30e+00 1.89e-01 1.43e+01 angle pdb=" C LYS L 50 " pdb=" N ALA L 51 " pdb=" CA ALA L 51 " ideal model delta sigma weight residual 121.54 126.98 -5.44 1.91e+00 2.74e-01 8.11e+00 angle pdb=" C VAL A 350 " pdb=" CA VAL A 350 " pdb=" CB VAL A 350 " ideal model delta sigma weight residual 112.26 109.09 3.17 1.62e+00 3.81e-01 3.83e+00 angle pdb=" N VAL A 350 " pdb=" CA VAL A 350 " pdb=" C VAL A 350 " ideal model delta sigma weight residual 111.09 113.30 -2.21 1.25e+00 6.40e-01 3.14e+00 angle pdb=" CA TYR L 91 " pdb=" CB TYR L 91 " pdb=" CG TYR L 91 " ideal model delta sigma weight residual 113.90 117.09 -3.19 1.80e+00 3.09e-01 3.13e+00 ... (remaining 4613 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 1741 17.68 - 35.37: 211 35.37 - 53.05: 44 53.05 - 70.73: 8 70.73 - 88.42: 2 Dihedral angle restraints: 2006 sinusoidal: 785 harmonic: 1221 Sorted by residual: dihedral pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " pdb=" SG CYS A 432 " pdb=" CB CYS A 432 " ideal model delta sinusoidal sigma weight residual 93.00 47.13 45.87 1 1.00e+01 1.00e-02 2.92e+01 dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 50.37 42.63 1 1.00e+01 1.00e-02 2.54e+01 dihedral pdb=" CA CYS A 432 " pdb=" C CYS A 432 " pdb=" N VAL A 433 " pdb=" CA VAL A 433 " ideal model delta harmonic sigma weight residual -180.00 -163.73 -16.27 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 2003 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 337 0.039 - 0.079: 113 0.079 - 0.118: 46 0.118 - 0.157: 2 0.157 - 0.197: 1 Chirality restraints: 499 Sorted by residual: chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 343 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.67e-01 chirality pdb=" CA ILE L 48 " pdb=" N ILE L 48 " pdb=" C ILE L 48 " pdb=" CB ILE L 48 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.82e-01 chirality pdb=" CA ILE A 434 " pdb=" N ILE A 434 " pdb=" C ILE A 434 " pdb=" CB ILE A 434 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.28e-01 ... (remaining 496 not shown) Planarity restraints: 587 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 383 " 0.034 5.00e-02 4.00e+02 5.25e-02 4.41e+00 pdb=" N PRO A 384 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 384 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 384 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE H 76 " 0.006 2.00e-02 2.50e+03 1.27e-02 1.62e+00 pdb=" C ILE H 76 " -0.022 2.00e-02 2.50e+03 pdb=" O ILE H 76 " 0.008 2.00e-02 2.50e+03 pdb=" N THR H 77 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 511 " 0.005 2.00e-02 2.50e+03 1.04e-02 1.08e+00 pdb=" C VAL A 511 " -0.018 2.00e-02 2.50e+03 pdb=" O VAL A 511 " 0.007 2.00e-02 2.50e+03 pdb=" N VAL A 512 " 0.006 2.00e-02 2.50e+03 ... (remaining 584 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 255 2.74 - 3.28: 3095 3.28 - 3.82: 5294 3.82 - 4.36: 6181 4.36 - 4.90: 11199 Nonbonded interactions: 26024 Sorted by model distance: nonbonded pdb=" O ASN A 439 " pdb=" OG SER A 443 " model vdw 2.198 3.040 nonbonded pdb=" OD2 ASP A 398 " pdb=" OH TYR A 423 " model vdw 2.223 3.040 nonbonded pdb=" OD1 ASP A 442 " pdb=" OH TYR A 451 " model vdw 2.240 3.040 nonbonded pdb=" O SER A 443 " pdb=" NH1 ARG H 59 " model vdw 2.251 3.120 nonbonded pdb=" O THR A 393 " pdb=" OG1 THR A 523 " model vdw 2.296 3.040 ... (remaining 26019 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 group one per residue 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: 0.160 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.060 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 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 0.042 3404 Z= 0.158 Angle : 0.546 8.708 4633 Z= 0.288 Chirality : 0.045 0.197 499 Planarity : 0.004 0.052 586 Dihedral : 15.592 88.416 1214 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.56 % Allowed : 24.79 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.30 (0.42), residues: 416 helix: -3.39 (0.77), residues: 27 sheet: 0.90 (0.45), residues: 153 loop : -0.53 (0.40), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 353 HIS 0.002 0.001 HIS H 110 PHE 0.011 0.001 PHE A 392 TYR 0.015 0.001 TYR L 91 ARG 0.004 0.000 ARG A 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00371 ( 1) link_NAG-ASN : angle 1.84265 ( 3) hydrogen bonds : bond 0.19924 ( 106) hydrogen bonds : angle 8.12244 ( 261) SS BOND : bond 0.00761 ( 6) SS BOND : angle 1.49047 ( 12) covalent geometry : bond 0.00361 ( 3397) covalent geometry : angle 0.53994 ( 4618) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 0.341 Fit side-chains REVERT: A 357 ARG cc_start: 0.7266 (ttt-90) cc_final: 0.6858 (ttm-80) REVERT: A 403 ARG cc_start: 0.7775 (ttp80) cc_final: 0.7560 (mtp180) REVERT: A 471 GLU cc_start: 0.6768 (mm-30) cc_final: 0.6402 (mm-30) REVERT: H 17 SER cc_start: 0.8227 (m) cc_final: 0.7955 (p) REVERT: H 19 MET cc_start: 0.7052 (ttm) cc_final: 0.6608 (ttp) REVERT: H 21 SER cc_start: 0.7327 (p) cc_final: 0.7057 (t) REVERT: L 69 THR cc_start: 0.7509 (p) cc_final: 0.7144 (m) outliers start: 2 outliers final: 2 residues processed: 52 average time/residue: 0.1673 time to fit residues: 10.7001 Evaluate side-chains 39 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 37 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 105 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 0.1980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 10.0000 chunk 12 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 chunk 23 optimal weight: 0.1980 chunk 37 optimal weight: 5.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN H 67 HIS L 6 GLN L 89 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.167605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.136858 restraints weight = 3529.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.138565 restraints weight = 2867.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.139982 restraints weight = 2503.938| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.1051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 3404 Z= 0.106 Angle : 0.512 7.824 4633 Z= 0.271 Chirality : 0.045 0.200 499 Planarity : 0.004 0.041 586 Dihedral : 5.331 55.637 488 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 4.79 % Allowed : 23.10 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.42), residues: 416 helix: -2.75 (0.87), residues: 27 sheet: 0.98 (0.45), residues: 156 loop : -0.43 (0.40), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 33 HIS 0.003 0.001 HIS H 110 PHE 0.007 0.001 PHE A 392 TYR 0.010 0.001 TYR L 91 ARG 0.003 0.000 ARG H 59 Details of bonding type rmsd link_NAG-ASN : bond 0.00519 ( 1) link_NAG-ASN : angle 1.69923 ( 3) hydrogen bonds : bond 0.02867 ( 106) hydrogen bonds : angle 5.62665 ( 261) SS BOND : bond 0.00776 ( 6) SS BOND : angle 1.45438 ( 12) covalent geometry : bond 0.00237 ( 3397) covalent geometry : angle 0.50579 ( 4618) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 38 time to evaluate : 0.371 Fit side-chains REVERT: A 357 ARG cc_start: 0.7521 (ttt-90) cc_final: 0.7033 (ttm-80) REVERT: A 462 LYS cc_start: 0.7118 (OUTLIER) cc_final: 0.6691 (mmtm) REVERT: L 5 THR cc_start: 0.7501 (m) cc_final: 0.6970 (t) outliers start: 17 outliers final: 11 residues processed: 54 average time/residue: 0.1548 time to fit residues: 10.4032 Evaluate side-chains 44 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 32 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 119 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 32 optimal weight: 20.0000 chunk 33 optimal weight: 1.9990 chunk 11 optimal weight: 0.0070 chunk 16 optimal weight: 0.1980 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 5 optimal weight: 0.5980 chunk 13 optimal weight: 9.9990 chunk 24 optimal weight: 0.9980 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.169856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.139297 restraints weight = 3447.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.140790 restraints weight = 2803.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.140790 restraints weight = 2465.537| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 3404 Z= 0.091 Angle : 0.481 7.136 4633 Z= 0.253 Chirality : 0.044 0.185 499 Planarity : 0.003 0.036 586 Dihedral : 4.460 32.328 487 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 5.63 % Allowed : 22.25 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.02 (0.42), residues: 416 helix: -2.45 (0.93), residues: 27 sheet: 0.98 (0.44), residues: 158 loop : -0.33 (0.40), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 33 HIS 0.002 0.000 HIS H 110 PHE 0.007 0.001 PHE A 392 TYR 0.010 0.001 TYR L 91 ARG 0.003 0.000 ARG H 59 Details of bonding type rmsd link_NAG-ASN : bond 0.00546 ( 1) link_NAG-ASN : angle 1.56149 ( 3) hydrogen bonds : bond 0.02539 ( 106) hydrogen bonds : angle 5.15606 ( 261) SS BOND : bond 0.00668 ( 6) SS BOND : angle 1.35282 ( 12) covalent geometry : bond 0.00206 ( 3397) covalent geometry : angle 0.47473 ( 4618) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 35 time to evaluate : 0.356 Fit side-chains REVERT: A 357 ARG cc_start: 0.7499 (ttt-90) cc_final: 0.7033 (ttm-80) REVERT: A 462 LYS cc_start: 0.7130 (OUTLIER) cc_final: 0.6746 (mmtm) REVERT: A 468 ILE cc_start: 0.7945 (OUTLIER) cc_final: 0.7700 (mt) REVERT: H 10 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.5704 (mp0) REVERT: L 5 THR cc_start: 0.7520 (m) cc_final: 0.6967 (t) outliers start: 20 outliers final: 11 residues processed: 54 average time/residue: 0.1434 time to fit residues: 9.7450 Evaluate side-chains 48 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 34 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain L residue 89 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.0670 chunk 22 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 36 optimal weight: 0.0980 chunk 38 optimal weight: 9.9990 chunk 40 optimal weight: 0.0770 chunk 21 optimal weight: 6.9990 chunk 11 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 overall best weight: 1.2480 ------------------------------------------------------------------------------- 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 = 0.3746 r_free = 0.3746 target = 0.166174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.136508 restraints weight = 3586.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.134863 restraints weight = 3411.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.136050 restraints weight = 3084.841| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3404 Z= 0.130 Angle : 0.527 8.256 4633 Z= 0.273 Chirality : 0.046 0.199 499 Planarity : 0.003 0.033 586 Dihedral : 4.619 31.895 486 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 5.63 % Allowed : 23.10 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.01 (0.42), residues: 416 helix: -2.19 (0.99), residues: 27 sheet: 1.13 (0.45), residues: 150 loop : -0.48 (0.39), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 353 HIS 0.002 0.000 HIS H 110 PHE 0.009 0.001 PHE L 71 TYR 0.013 0.001 TYR L 91 ARG 0.004 0.000 ARG A 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00614 ( 1) link_NAG-ASN : angle 2.00961 ( 3) hydrogen bonds : bond 0.02603 ( 106) hydrogen bonds : angle 5.08181 ( 261) SS BOND : bond 0.00780 ( 6) SS BOND : angle 1.51862 ( 12) covalent geometry : bond 0.00308 ( 3397) covalent geometry : angle 0.51976 ( 4618) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 31 time to evaluate : 0.309 Fit side-chains REVERT: A 357 ARG cc_start: 0.7524 (ttt-90) cc_final: 0.7078 (ttm-80) REVERT: A 462 LYS cc_start: 0.7267 (OUTLIER) cc_final: 0.6819 (mmtm) REVERT: A 468 ILE cc_start: 0.8051 (OUTLIER) cc_final: 0.7821 (mt) REVERT: H 10 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.5696 (mp0) outliers start: 20 outliers final: 14 residues processed: 50 average time/residue: 0.1265 time to fit residues: 8.1798 Evaluate side-chains 47 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 30 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 89 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 25 optimal weight: 0.7980 chunk 14 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 30 optimal weight: 0.0980 chunk 3 optimal weight: 9.9990 chunk 32 optimal weight: 20.0000 chunk 20 optimal weight: 0.0870 chunk 6 optimal weight: 3.9990 overall best weight: 0.5962 ------------------------------------------------------------------------------- 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 = 0.3781 r_free = 0.3781 target = 0.169802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.138497 restraints weight = 3492.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.140456 restraints weight = 2798.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.141322 restraints weight = 2412.488| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 3404 Z= 0.090 Angle : 0.482 7.370 4633 Z= 0.251 Chirality : 0.044 0.189 499 Planarity : 0.003 0.031 586 Dihedral : 4.413 31.065 486 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 5.07 % Allowed : 23.10 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.16 (0.42), residues: 416 helix: -1.44 (1.29), residues: 19 sheet: 0.90 (0.44), residues: 158 loop : -0.27 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 33 HIS 0.002 0.000 HIS H 110 PHE 0.007 0.001 PHE A 392 TYR 0.008 0.001 TYR A 365 ARG 0.003 0.000 ARG A 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00527 ( 1) link_NAG-ASN : angle 1.62744 ( 3) hydrogen bonds : bond 0.02353 ( 106) hydrogen bonds : angle 4.93050 ( 261) SS BOND : bond 0.00678 ( 6) SS BOND : angle 1.33974 ( 12) covalent geometry : bond 0.00206 ( 3397) covalent geometry : angle 0.47564 ( 4618) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 33 time to evaluate : 0.292 Fit side-chains REVERT: A 357 ARG cc_start: 0.7471 (ttt-90) cc_final: 0.7091 (ttm-80) REVERT: A 396 TYR cc_start: 0.7833 (m-80) cc_final: 0.7440 (m-80) REVERT: A 462 LYS cc_start: 0.7246 (OUTLIER) cc_final: 0.6803 (mmtm) REVERT: H 10 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.5625 (mp0) REVERT: L 88 CYS cc_start: 0.7279 (p) cc_final: 0.6847 (p) outliers start: 18 outliers final: 15 residues processed: 50 average time/residue: 0.1182 time to fit residues: 7.7329 Evaluate side-chains 50 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 33 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 89 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 3 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 = 0.3756 r_free = 0.3756 target = 0.167227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.135164 restraints weight = 3568.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.137387 restraints weight = 2848.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.138544 restraints weight = 2471.724| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3404 Z= 0.127 Angle : 0.515 8.154 4633 Z= 0.267 Chirality : 0.045 0.197 499 Planarity : 0.003 0.030 586 Dihedral : 4.566 31.083 486 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 7.32 % Allowed : 20.85 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.16 (0.42), residues: 416 helix: -1.29 (1.34), residues: 19 sheet: 1.08 (0.44), residues: 151 loop : -0.39 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 353 HIS 0.002 0.001 HIS H 110 PHE 0.010 0.001 PHE H 109 TYR 0.012 0.001 TYR L 91 ARG 0.002 0.000 ARG A 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00588 ( 1) link_NAG-ASN : angle 1.98646 ( 3) hydrogen bonds : bond 0.02502 ( 106) hydrogen bonds : angle 4.96477 ( 261) SS BOND : bond 0.00772 ( 6) SS BOND : angle 1.51687 ( 12) covalent geometry : bond 0.00302 ( 3397) covalent geometry : angle 0.50792 ( 4618) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 33 time to evaluate : 0.326 Fit side-chains REVERT: A 357 ARG cc_start: 0.7489 (ttt-90) cc_final: 0.7072 (ttm-80) REVERT: A 462 LYS cc_start: 0.7327 (OUTLIER) cc_final: 0.6828 (mmtm) REVERT: A 468 ILE cc_start: 0.8078 (OUTLIER) cc_final: 0.7849 (mt) REVERT: H 10 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.5632 (mp0) REVERT: H 39 GLN cc_start: 0.7694 (OUTLIER) cc_final: 0.7289 (tt0) REVERT: L 5 THR cc_start: 0.7673 (m) cc_final: 0.7431 (m) REVERT: L 42 LYS cc_start: 0.7165 (mtpp) cc_final: 0.6918 (mtpp) outliers start: 26 outliers final: 20 residues processed: 57 average time/residue: 0.1301 time to fit residues: 9.4889 Evaluate side-chains 55 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 31 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 89 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 1 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 25 optimal weight: 0.2980 chunk 23 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.169518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.138432 restraints weight = 3487.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.140421 restraints weight = 2808.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.141884 restraints weight = 2432.751| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 3404 Z= 0.095 Angle : 0.514 7.881 4633 Z= 0.262 Chirality : 0.045 0.268 499 Planarity : 0.003 0.029 586 Dihedral : 4.685 37.180 486 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 5.92 % Allowed : 21.97 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.23 (0.43), residues: 416 helix: -1.18 (1.37), residues: 19 sheet: 0.94 (0.43), residues: 158 loop : -0.24 (0.41), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 353 HIS 0.002 0.000 HIS H 110 PHE 0.007 0.001 PHE A 392 TYR 0.009 0.001 TYR L 91 ARG 0.002 0.000 ARG A 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00722 ( 1) link_NAG-ASN : angle 5.39488 ( 3) hydrogen bonds : bond 0.02357 ( 106) hydrogen bonds : angle 4.95705 ( 261) SS BOND : bond 0.00687 ( 6) SS BOND : angle 1.36108 ( 12) covalent geometry : bond 0.00220 ( 3397) covalent geometry : angle 0.49137 ( 4618) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 33 time to evaluate : 0.367 Fit side-chains REVERT: A 357 ARG cc_start: 0.7469 (ttt-90) cc_final: 0.7090 (ttm-80) REVERT: A 396 TYR cc_start: 0.7824 (m-80) cc_final: 0.7419 (m-80) REVERT: A 462 LYS cc_start: 0.7300 (OUTLIER) cc_final: 0.6818 (mmtm) REVERT: A 468 ILE cc_start: 0.7974 (OUTLIER) cc_final: 0.7740 (mt) REVERT: H 10 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.5694 (mp0) REVERT: H 97 THR cc_start: 0.9469 (m) cc_final: 0.9102 (p) REVERT: L 50 LYS cc_start: 0.8134 (mmtm) cc_final: 0.7854 (mmtm) outliers start: 21 outliers final: 17 residues processed: 53 average time/residue: 0.1529 time to fit residues: 10.0639 Evaluate side-chains 50 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 30 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 89 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 35 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 14 optimal weight: 8.9990 chunk 17 optimal weight: 0.0470 chunk 11 optimal weight: 1.9990 chunk 36 optimal weight: 0.3980 chunk 26 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 overall best weight: 2.0884 ------------------------------------------------------------------------------- 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 = 0.3722 r_free = 0.3722 target = 0.163955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.132460 restraints weight = 3516.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.134143 restraints weight = 2854.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.135612 restraints weight = 2511.149| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3404 Z= 0.186 Angle : 0.612 9.553 4633 Z= 0.310 Chirality : 0.048 0.213 499 Planarity : 0.004 0.029 586 Dihedral : 5.272 44.488 486 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 7.32 % Allowed : 20.00 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.08 (0.42), residues: 416 helix: -1.27 (1.33), residues: 19 sheet: 1.04 (0.43), residues: 151 loop : -0.46 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 353 HIS 0.003 0.001 HIS H 110 PHE 0.010 0.002 PHE A 347 TYR 0.015 0.001 TYR L 91 ARG 0.005 0.000 ARG A 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00501 ( 1) link_NAG-ASN : angle 6.95601 ( 3) hydrogen bonds : bond 0.02809 ( 106) hydrogen bonds : angle 5.26394 ( 261) SS BOND : bond 0.00920 ( 6) SS BOND : angle 1.76766 ( 12) covalent geometry : bond 0.00443 ( 3397) covalent geometry : angle 0.58002 ( 4618) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 33 time to evaluate : 0.356 Fit side-chains REVERT: A 357 ARG cc_start: 0.7523 (ttt-90) cc_final: 0.7141 (ttm-80) REVERT: A 462 LYS cc_start: 0.7349 (OUTLIER) cc_final: 0.6967 (mmtt) REVERT: A 468 ILE cc_start: 0.8116 (OUTLIER) cc_final: 0.7899 (mt) REVERT: H 10 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.5697 (mp0) REVERT: H 39 GLN cc_start: 0.7682 (OUTLIER) cc_final: 0.7313 (tt0) REVERT: L 5 THR cc_start: 0.7629 (m) cc_final: 0.7401 (m) outliers start: 26 outliers final: 20 residues processed: 57 average time/residue: 0.1200 time to fit residues: 8.9536 Evaluate side-chains 55 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 31 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 89 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 9 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 26 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 36 optimal weight: 0.0570 chunk 28 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 overall best weight: 0.9302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.167739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.136791 restraints weight = 3497.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.138513 restraints weight = 2844.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.139977 restraints weight = 2496.117| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3404 Z= 0.112 Angle : 0.563 8.727 4633 Z= 0.284 Chirality : 0.046 0.218 499 Planarity : 0.003 0.029 586 Dihedral : 5.358 48.196 486 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 5.63 % Allowed : 22.82 % Favored : 71.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.01 (0.42), residues: 416 helix: -2.07 (1.04), residues: 27 sheet: 1.01 (0.43), residues: 151 loop : -0.41 (0.41), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 353 HIS 0.002 0.001 HIS H 110 PHE 0.013 0.001 PHE A 342 TYR 0.010 0.001 TYR L 91 ARG 0.004 0.000 ARG A 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00960 ( 1) link_NAG-ASN : angle 7.48855 ( 3) hydrogen bonds : bond 0.02530 ( 106) hydrogen bonds : angle 5.32688 ( 261) SS BOND : bond 0.00773 ( 6) SS BOND : angle 1.48025 ( 12) covalent geometry : bond 0.00261 ( 3397) covalent geometry : angle 0.52500 ( 4618) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 31 time to evaluate : 0.325 Fit side-chains REVERT: A 357 ARG cc_start: 0.7488 (ttt-90) cc_final: 0.7087 (ttm-80) REVERT: A 462 LYS cc_start: 0.7326 (OUTLIER) cc_final: 0.6804 (mmtm) REVERT: A 468 ILE cc_start: 0.7986 (OUTLIER) cc_final: 0.7759 (mt) REVERT: H 10 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.5578 (mp0) REVERT: H 97 THR cc_start: 0.9456 (m) cc_final: 0.9061 (p) outliers start: 20 outliers final: 17 residues processed: 49 average time/residue: 0.1366 time to fit residues: 8.5039 Evaluate side-chains 50 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 30 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 89 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 29 optimal weight: 2.9990 chunk 14 optimal weight: 8.9990 chunk 30 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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 = 0.3731 r_free = 0.3731 target = 0.164765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.133849 restraints weight = 3488.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.135577 restraints weight = 2905.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.136373 restraints weight = 2545.807| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3404 Z= 0.163 Angle : 0.592 9.319 4633 Z= 0.300 Chirality : 0.047 0.228 499 Planarity : 0.004 0.029 586 Dihedral : 5.374 45.643 486 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 6.48 % Allowed : 22.25 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.04 (0.42), residues: 416 helix: -1.30 (1.32), residues: 19 sheet: 0.96 (0.43), residues: 151 loop : -0.45 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 353 HIS 0.002 0.001 HIS H 110 PHE 0.008 0.001 PHE H 109 TYR 0.014 0.001 TYR L 91 ARG 0.005 0.000 ARG A 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00211 ( 1) link_NAG-ASN : angle 6.34449 ( 3) hydrogen bonds : bond 0.02732 ( 106) hydrogen bonds : angle 5.25367 ( 261) SS BOND : bond 0.00881 ( 6) SS BOND : angle 1.69536 ( 12) covalent geometry : bond 0.00389 ( 3397) covalent geometry : angle 0.56361 ( 4618) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 35 time to evaluate : 0.338 Fit side-chains REVERT: A 357 ARG cc_start: 0.7513 (ttt-90) cc_final: 0.7151 (ttm-80) REVERT: A 358 ILE cc_start: 0.6472 (OUTLIER) cc_final: 0.6182 (mp) REVERT: A 462 LYS cc_start: 0.7365 (OUTLIER) cc_final: 0.6999 (mmtt) REVERT: A 468 ILE cc_start: 0.8060 (OUTLIER) cc_final: 0.7837 (mt) REVERT: H 10 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.5665 (mp0) REVERT: L 5 THR cc_start: 0.7649 (m) cc_final: 0.7412 (m) outliers start: 23 outliers final: 18 residues processed: 56 average time/residue: 0.1296 time to fit residues: 9.2479 Evaluate side-chains 57 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 35 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 89 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 31 optimal weight: 6.9990 chunk 4 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 24 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 = 0.3737 r_free = 0.3737 target = 0.165100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.134140 restraints weight = 3521.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.135691 restraints weight = 2889.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.137240 restraints weight = 2539.206| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3404 Z= 0.156 Angle : 0.586 9.537 4633 Z= 0.299 Chirality : 0.047 0.235 499 Planarity : 0.004 0.033 586 Dihedral : 5.427 44.804 486 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 7.04 % Allowed : 21.69 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.03 (0.41), residues: 416 helix: -1.34 (1.28), residues: 19 sheet: 0.89 (0.43), residues: 151 loop : -0.49 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 353 HIS 0.002 0.001 HIS H 110 PHE 0.008 0.001 PHE A 347 TYR 0.013 0.001 TYR L 91 ARG 0.005 0.000 ARG A 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00380 ( 1) link_NAG-ASN : angle 5.90557 ( 3) hydrogen bonds : bond 0.02735 ( 106) hydrogen bonds : angle 5.26070 ( 261) SS BOND : bond 0.00874 ( 6) SS BOND : angle 1.69512 ( 12) covalent geometry : bond 0.00372 ( 3397) covalent geometry : angle 0.56080 ( 4618) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1481.68 seconds wall clock time: 26 minutes 30.58 seconds (1590.58 seconds total)