Starting phenix.real_space_refine on Wed Jul 23 12:24:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y6l_33643/07_2025/7y6l_33643.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y6l_33643/07_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_33643/07_2025/7y6l_33643.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y6l_33643/07_2025/7y6l_33643.map" model { file = "/net/cci-nas-00/data/ceres_data/7y6l_33643/07_2025/7y6l_33643.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y6l_33643/07_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-5711/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: 2.67, per 1000 atoms: 0.81 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 395.8 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: 0.41 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: 0.86 Time building geometry restraints manager: 0.92 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: 0.430 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.910 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.510 ------------------------------------------------------------------------------- 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 : 0.271 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: 0.1772 time to fit residues: 11.1964 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 : 0.396 ------------------------------------------------------------------------------- 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: 1.9990 chunk 19 optimal weight: 6.9990 chunk 23 optimal weight: 0.1980 chunk 37 optimal weight: 5.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.3750 r_free = 0.3750 target = 0.166503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.135608 restraints weight = 3546.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.137316 restraints weight = 2860.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.138783 restraints weight = 2498.910| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.1056 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= 0.116 Angle : 0.522 8.124 4633 Z= 0.275 Chirality : 0.045 0.199 499 Planarity : 0.004 0.041 586 Dihedral : 5.165 46.127 488 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 4.51 % Allowed : 22.54 % Favored : 72.96 % 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: -0.12 (0.42), residues: 416 helix: -2.76 (0.87), residues: 27 sheet: 1.02 (0.45), residues: 155 loop : -0.48 (0.40), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 33 HIS 0.003 0.001 HIS H 110 PHE 0.007 0.001 PHE A 392 TYR 0.011 0.001 TYR L 91 ARG 0.003 0.000 ARG H 59 Details of bonding type rmsd link_NAG-ASN : bond 0.00524 ( 1) link_NAG-ASN : angle 1.79986 ( 3) hydrogen bonds : bond 0.02964 ( 106) hydrogen bonds : angle 5.61960 ( 261) SS BOND : bond 0.00800 ( 6) SS BOND : angle 1.49659 ( 12) covalent geometry : bond 0.00266 ( 3397) covalent geometry : angle 0.51485 ( 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 53 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 37 time to evaluate : 0.319 Fit side-chains REVERT: A 357 ARG cc_start: 0.7534 (ttt-90) cc_final: 0.7056 (ttm-80) REVERT: A 462 LYS cc_start: 0.7112 (OUTLIER) cc_final: 0.6701 (mmtm) outliers start: 16 outliers final: 10 residues processed: 52 average time/residue: 0.1466 time to fit residues: 9.5999 Evaluate side-chains 42 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 31 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 393 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 462 LYS 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: 4.9990 chunk 28 optimal weight: 4.9990 chunk 32 optimal weight: 20.0000 chunk 33 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 37 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 24 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 = 0.3683 r_free = 0.3683 target = 0.160282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.129301 restraints weight = 3542.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.130914 restraints weight = 2905.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.131812 restraints weight = 2561.544| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 3404 Z= 0.254 Angle : 0.653 11.319 4633 Z= 0.341 Chirality : 0.050 0.219 499 Planarity : 0.005 0.040 586 Dihedral : 5.466 37.346 487 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 7.32 % Allowed : 21.69 % Favored : 70.99 % 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: -0.42 (0.41), residues: 416 helix: -2.87 (0.81), residues: 27 sheet: 0.81 (0.44), residues: 152 loop : -0.68 (0.39), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 33 HIS 0.004 0.001 HIS H 110 PHE 0.016 0.002 PHE A 347 TYR 0.018 0.002 TYR L 91 ARG 0.003 0.001 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00585 ( 1) link_NAG-ASN : angle 2.93333 ( 3) hydrogen bonds : bond 0.03425 ( 106) hydrogen bonds : angle 5.61686 ( 261) SS BOND : bond 0.01071 ( 6) SS BOND : angle 2.06269 ( 12) covalent geometry : bond 0.00608 ( 3397) covalent geometry : angle 0.64095 ( 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 62 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 36 time to evaluate : 0.337 Fit side-chains REVERT: A 357 ARG cc_start: 0.7583 (ttt-90) cc_final: 0.7184 (ttm-80) REVERT: A 390 LEU cc_start: 0.5506 (OUTLIER) cc_final: 0.5255 (tp) REVERT: A 454 ARG cc_start: 0.8373 (ttm-80) cc_final: 0.7372 (ttm-80) REVERT: A 462 LYS cc_start: 0.7369 (OUTLIER) cc_final: 0.6996 (mmtt) REVERT: H 10 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.5871 (mp0) REVERT: H 39 GLN cc_start: 0.7703 (OUTLIER) cc_final: 0.7324 (tt0) outliers start: 26 outliers final: 18 residues processed: 58 average time/residue: 0.1484 time to fit residues: 10.8408 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 : 0.599 ------------------------------------------------------------------------------- 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 390 LEU 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 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 100 THR Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 103 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 19 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 38 optimal weight: 7.9990 chunk 40 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 3 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 = 0.3717 r_free = 0.3717 target = 0.163322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.132293 restraints weight = 3599.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.133946 restraints weight = 2944.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.134891 restraints weight = 2576.830| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3404 Z= 0.150 Angle : 0.565 10.280 4633 Z= 0.293 Chirality : 0.047 0.208 499 Planarity : 0.004 0.038 586 Dihedral : 5.068 36.747 486 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 7.32 % Allowed : 22.25 % Favored : 70.42 % 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: -0.37 (0.41), residues: 416 helix: -2.60 (0.87), residues: 27 sheet: 0.76 (0.44), residues: 152 loop : -0.62 (0.39), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 33 HIS 0.002 0.001 HIS H 110 PHE 0.009 0.001 PHE L 71 TYR 0.013 0.001 TYR L 91 ARG 0.002 0.000 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00559 ( 1) link_NAG-ASN : angle 2.23957 ( 3) hydrogen bonds : bond 0.02884 ( 106) hydrogen bonds : angle 5.37309 ( 261) SS BOND : bond 0.00892 ( 6) SS BOND : angle 1.74828 ( 12) covalent geometry : bond 0.00356 ( 3397) covalent geometry : angle 0.55577 ( 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 62 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 36 time to evaluate : 0.720 Fit side-chains REVERT: A 357 ARG cc_start: 0.7583 (ttt-90) cc_final: 0.7175 (ttm-80) REVERT: A 358 ILE cc_start: 0.6568 (OUTLIER) cc_final: 0.6243 (mp) REVERT: A 462 LYS cc_start: 0.7324 (OUTLIER) cc_final: 0.6957 (mmtt) REVERT: H 10 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.5673 (mp0) outliers start: 26 outliers final: 17 residues processed: 61 average time/residue: 0.2457 time to fit residues: 18.7114 Evaluate side-chains 54 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 34 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR 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 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 89 SER Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain L residue 46 VAL 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: 0.8980 chunk 14 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 36 optimal weight: 0.0770 chunk 23 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 30 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 chunk 32 optimal weight: 20.0000 chunk 20 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.3142 ------------------------------------------------------------------------------- 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 = 0.3719 r_free = 0.3719 target = 0.163687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.132920 restraints weight = 3540.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.134479 restraints weight = 2916.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.135093 restraints weight = 2578.638| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 3404 Z= 0.137 Angle : 0.565 10.057 4633 Z= 0.288 Chirality : 0.047 0.266 499 Planarity : 0.004 0.035 586 Dihedral : 5.118 41.129 486 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 7.89 % Allowed : 21.69 % Favored : 70.42 % 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: -0.34 (0.41), residues: 416 helix: -2.54 (0.91), residues: 27 sheet: 0.82 (0.43), residues: 151 loop : -0.62 (0.39), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 33 HIS 0.002 0.001 HIS H 110 PHE 0.008 0.001 PHE H 109 TYR 0.013 0.001 TYR A 369 ARG 0.007 0.000 ARG A 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00583 ( 1) link_NAG-ASN : angle 5.41745 ( 3) hydrogen bonds : bond 0.02787 ( 106) hydrogen bonds : angle 5.30910 ( 261) SS BOND : bond 0.00839 ( 6) SS BOND : angle 1.66648 ( 12) covalent geometry : bond 0.00325 ( 3397) covalent geometry : angle 0.54196 ( 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 63 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 35 time to evaluate : 0.342 Fit side-chains REVERT: A 357 ARG cc_start: 0.7608 (ttt-90) cc_final: 0.7171 (ttm-80) REVERT: A 462 LYS cc_start: 0.7328 (OUTLIER) cc_final: 0.6959 (mmtt) REVERT: H 10 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.5669 (mp0) outliers start: 28 outliers final: 21 residues processed: 60 average time/residue: 0.1336 time to fit residues: 10.1911 Evaluate side-chains 55 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 32 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR 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 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 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 11 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: 9.9990 chunk 35 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 21 optimal weight: 6.9990 chunk 36 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 8 optimal weight: 0.0470 overall best weight: 1.6082 ------------------------------------------------------------------------------- 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 = 0.3720 r_free = 0.3720 target = 0.163643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.132449 restraints weight = 3585.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.134062 restraints weight = 2929.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.135570 restraints weight = 2563.126| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 3404 Z= 0.156 Angle : 0.588 10.372 4633 Z= 0.299 Chirality : 0.047 0.216 499 Planarity : 0.004 0.032 586 Dihedral : 5.229 43.586 486 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 7.32 % Allowed : 21.69 % Favored : 70.99 % 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: -0.20 (0.41), residues: 416 helix: -1.82 (1.18), residues: 19 sheet: 0.79 (0.43), residues: 151 loop : -0.57 (0.39), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 33 HIS 0.002 0.001 HIS H 110 PHE 0.008 0.001 PHE L 83 TYR 0.014 0.001 TYR A 369 ARG 0.005 0.000 ARG A 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00475 ( 1) link_NAG-ASN : angle 5.88707 ( 3) hydrogen bonds : bond 0.02858 ( 106) hydrogen bonds : angle 5.37085 ( 261) SS BOND : bond 0.00871 ( 6) SS BOND : angle 1.75594 ( 12) covalent geometry : bond 0.00373 ( 3397) covalent geometry : angle 0.56261 ( 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 : 0.361 Fit side-chains REVERT: A 357 ARG cc_start: 0.7613 (ttt-90) cc_final: 0.7164 (ttm-80) REVERT: A 462 LYS cc_start: 0.7362 (OUTLIER) cc_final: 0.7000 (mmtt) REVERT: H 10 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.5703 (mp0) REVERT: H 39 GLN cc_start: 0.7697 (OUTLIER) cc_final: 0.7303 (tt0) outliers start: 26 outliers final: 22 residues processed: 55 average time/residue: 0.1263 time to fit residues: 9.0320 Evaluate side-chains 57 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 32 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR 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 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 11 LEU 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: 0.7980 chunk 22 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 7 optimal weight: 0.4980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3754 r_free = 0.3754 target = 0.167163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.136695 restraints weight = 3510.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.138726 restraints weight = 2834.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.139787 restraints weight = 2473.963| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 3404 Z= 0.103 Angle : 0.541 9.367 4633 Z= 0.276 Chirality : 0.045 0.185 499 Planarity : 0.003 0.030 586 Dihedral : 5.261 47.656 486 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 6.76 % Allowed : 22.82 % Favored : 70.42 % 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: -0.15 (0.42), residues: 416 helix: -2.11 (1.02), residues: 25 sheet: 0.90 (0.43), residues: 151 loop : -0.51 (0.40), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 33 HIS 0.001 0.000 HIS H 110 PHE 0.007 0.001 PHE A 515 TYR 0.011 0.001 TYR A 369 ARG 0.005 0.000 ARG A 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00705 ( 1) link_NAG-ASN : angle 5.98373 ( 3) hydrogen bonds : bond 0.02599 ( 106) hydrogen bonds : angle 5.26037 ( 261) SS BOND : bond 0.00742 ( 6) SS BOND : angle 1.51306 ( 12) covalent geometry : bond 0.00240 ( 3397) covalent geometry : angle 0.51417 ( 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 58 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 34 time to evaluate : 0.353 Fit side-chains REVERT: A 357 ARG cc_start: 0.7563 (ttt-90) cc_final: 0.7100 (ttm-80) REVERT: A 462 LYS cc_start: 0.7405 (OUTLIER) cc_final: 0.7007 (mmtt) REVERT: H 10 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.5612 (mp0) REVERT: H 97 THR cc_start: 0.9477 (m) cc_final: 0.9083 (p) REVERT: L 5 THR cc_start: 0.7378 (m) cc_final: 0.6902 (t) outliers start: 24 outliers final: 19 residues processed: 54 average time/residue: 0.1551 time to fit residues: 10.8001 Evaluate side-chains 51 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 30 time to evaluate : 0.378 ------------------------------------------------------------------------------- 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 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 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 11 LEU 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: 4.9990 chunk 24 optimal weight: 0.7980 chunk 14 optimal weight: 7.9990 chunk 17 optimal weight: 0.2980 chunk 11 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 32 optimal weight: 20.0000 chunk 37 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 = 0.3769 r_free = 0.3769 target = 0.168721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.139985 restraints weight = 3457.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.137990 restraints weight = 3142.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.139725 restraints weight = 2941.052| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3404 Z= 0.106 Angle : 0.566 10.054 4633 Z= 0.283 Chirality : 0.045 0.182 499 Planarity : 0.003 0.028 586 Dihedral : 5.519 50.265 486 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 7.04 % Allowed : 21.97 % Favored : 70.99 % 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: -2.09 (1.01), residues: 25 sheet: 0.97 (0.44), residues: 151 loop : -0.48 (0.40), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 33 HIS 0.001 0.000 HIS H 110 PHE 0.010 0.001 PHE A 342 TYR 0.011 0.001 TYR A 369 ARG 0.004 0.000 ARG A 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00587 ( 1) link_NAG-ASN : angle 8.29974 ( 3) hydrogen bonds : bond 0.02570 ( 106) hydrogen bonds : angle 5.28781 ( 261) SS BOND : bond 0.00730 ( 6) SS BOND : angle 1.52734 ( 12) covalent geometry : bond 0.00249 ( 3397) covalent geometry : angle 0.52046 ( 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 58 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 33 time to evaluate : 0.330 Fit side-chains REVERT: A 357 ARG cc_start: 0.7557 (ttt-90) cc_final: 0.7118 (ttm-80) REVERT: A 358 ILE cc_start: 0.6480 (OUTLIER) cc_final: 0.6268 (mp) REVERT: A 462 LYS cc_start: 0.7413 (OUTLIER) cc_final: 0.7026 (mmtt) REVERT: H 10 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.5588 (mp0) REVERT: H 97 THR cc_start: 0.9469 (m) cc_final: 0.9059 (p) outliers start: 25 outliers final: 20 residues processed: 55 average time/residue: 0.1199 time to fit residues: 8.5875 Evaluate side-chains 55 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 32 time to evaluate : 0.327 ------------------------------------------------------------------------------- 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 444 LYS Chi-restraints excluded: chain A residue 462 LYS 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 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 11 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 75 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 9 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 26 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 37 optimal weight: 0.0020 chunk 33 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 overall best weight: 1.1192 ------------------------------------------------------------------------------- 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 = 0.3753 r_free = 0.3753 target = 0.166962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.135899 restraints weight = 3504.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.137579 restraints weight = 2827.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.139121 restraints weight = 2475.794| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3404 Z= 0.124 Angle : 0.563 9.585 4633 Z= 0.287 Chirality : 0.046 0.206 499 Planarity : 0.003 0.029 586 Dihedral : 5.324 45.733 486 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 7.32 % Allowed : 21.13 % 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: 0.11 (0.42), residues: 416 helix: -1.51 (1.24), residues: 19 sheet: 0.96 (0.44), residues: 151 loop : -0.34 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 33 HIS 0.001 0.001 HIS H 110 PHE 0.006 0.001 PHE A 392 TYR 0.012 0.001 TYR A 369 ARG 0.004 0.000 ARG A 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00414 ( 1) link_NAG-ASN : angle 6.31505 ( 3) hydrogen bonds : bond 0.02588 ( 106) hydrogen bonds : angle 5.30013 ( 261) SS BOND : bond 0.00783 ( 6) SS BOND : angle 1.61638 ( 12) covalent geometry : bond 0.00294 ( 3397) covalent geometry : angle 0.53465 ( 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 60 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 34 time to evaluate : 0.349 Fit side-chains REVERT: A 357 ARG cc_start: 0.7585 (ttt-90) cc_final: 0.7126 (ttm-80) REVERT: A 358 ILE cc_start: 0.6479 (OUTLIER) cc_final: 0.6245 (mp) REVERT: A 462 LYS cc_start: 0.7429 (OUTLIER) cc_final: 0.7043 (mmtt) REVERT: H 10 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.5687 (mp0) REVERT: H 39 GLN cc_start: 0.7649 (OUTLIER) cc_final: 0.7231 (tt0) outliers start: 26 outliers final: 20 residues processed: 57 average time/residue: 0.1385 time to fit residues: 9.9800 Evaluate side-chains 57 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 33 time to evaluate : 0.359 ------------------------------------------------------------------------------- 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 444 LYS Chi-restraints excluded: chain A residue 462 LYS 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 39 GLN 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 11 LEU 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: 4.9990 chunk 14 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 9 optimal weight: 0.0870 chunk 35 optimal weight: 3.9990 overall best weight: 0.9762 ------------------------------------------------------------------------------- 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 = 0.3761 r_free = 0.3761 target = 0.167668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.136392 restraints weight = 3453.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.138037 restraints weight = 2794.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.139403 restraints weight = 2451.158| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3404 Z= 0.115 Angle : 0.557 9.429 4633 Z= 0.283 Chirality : 0.046 0.215 499 Planarity : 0.003 0.028 586 Dihedral : 5.237 44.441 486 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 6.76 % Allowed : 22.25 % Favored : 70.99 % 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: 0.14 (0.42), residues: 416 helix: -1.53 (1.22), residues: 19 sheet: 0.98 (0.44), residues: 151 loop : -0.31 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 33 HIS 0.001 0.000 HIS H 110 PHE 0.007 0.001 PHE A 392 TYR 0.012 0.001 TYR A 369 ARG 0.007 0.000 ARG A 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00343 ( 1) link_NAG-ASN : angle 5.45124 ( 3) hydrogen bonds : bond 0.02546 ( 106) hydrogen bonds : angle 5.27545 ( 261) SS BOND : bond 0.00751 ( 6) SS BOND : angle 1.55114 ( 12) covalent geometry : bond 0.00271 ( 3397) covalent geometry : angle 0.53447 ( 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 57 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 33 time to evaluate : 0.356 Fit side-chains REVERT: A 357 ARG cc_start: 0.7566 (ttt-90) cc_final: 0.7108 (ttm-80) REVERT: A 358 ILE cc_start: 0.6464 (OUTLIER) cc_final: 0.6247 (mp) REVERT: A 462 LYS cc_start: 0.7423 (OUTLIER) cc_final: 0.7046 (mmtt) REVERT: H 10 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.5678 (mp0) REVERT: H 39 GLN cc_start: 0.7620 (OUTLIER) cc_final: 0.7305 (tt0) REVERT: H 97 THR cc_start: 0.9455 (m) cc_final: 0.9043 (p) outliers start: 24 outliers final: 19 residues processed: 54 average time/residue: 0.1305 time to fit residues: 9.0573 Evaluate side-chains 55 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 32 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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 444 LYS Chi-restraints excluded: chain A residue 462 LYS 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 39 GLN 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 11 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 75 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 31 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 13 optimal weight: 8.9990 chunk 30 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 = 0.3716 r_free = 0.3716 target = 0.163169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.132264 restraints weight = 3526.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.133924 restraints weight = 2899.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.135017 restraints weight = 2553.826| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 3404 Z= 0.194 Angle : 0.630 10.700 4633 Z= 0.319 Chirality : 0.048 0.208 499 Planarity : 0.004 0.027 586 Dihedral : 5.718 45.414 486 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 7.04 % Allowed : 21.97 % Favored : 70.99 % 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 (0.41), residues: 416 helix: -1.78 (1.13), residues: 19 sheet: 0.81 (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 0.003 0.001 HIS H 67 PHE 0.009 0.002 PHE A 347 TYR 0.018 0.002 TYR L 91 ARG 0.009 0.001 ARG A 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00157 ( 1) link_NAG-ASN : angle 6.41486 ( 3) hydrogen bonds : bond 0.02921 ( 106) hydrogen bonds : angle 5.43714 ( 261) SS BOND : bond 0.00926 ( 6) SS BOND : angle 1.94389 ( 12) covalent geometry : bond 0.00463 ( 3397) covalent geometry : angle 0.60146 ( 4618) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1603.32 seconds wall clock time: 29 minutes 7.68 seconds (1747.68 seconds total)