Starting phenix.real_space_refine on Thu Jul 2 00:37:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7eya_31380/07_2026/7eya_31380.cif Found real_map, /net/cci-nas-00/data/ceres_data/7eya_31380/07_2026/7eya_31380.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7eya_31380/07_2026/7eya_31380.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7eya_31380/07_2026/7eya_31380.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7eya_31380/07_2026/7eya_31380.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7eya_31380/07_2026/7eya_31380.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7eya_31380/07_2026/7eya_31380.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7eya_31380/07_2026/7eya_31380.map" } resolution = 3.77 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.022 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 18 5.16 5 C 2970 2.51 5 N 756 2.21 5 O 885 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4629 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 1465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1465 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 9, 'TRANS': 173} Chain: "L" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 801 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "H" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 965 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 2, 'TRANS': 122} Chain: "N" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1359 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 8, 'TRANS': 156} Chain breaks: 7 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 1.27, per 1000 atoms: 0.27 Number of scatterers: 4629 At special positions: 0 Unit cell: (73.03, 95.92, 98.1, 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 18 16.00 O 885 8.00 N 756 7.00 C 2970 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS R 336 " - pdb=" SG CYS R 361 " distance=2.03 Simple disulfide: pdb=" SG CYS R 379 " - pdb=" SG CYS R 432 " distance=2.05 Simple disulfide: pdb=" SG CYS R 480 " - pdb=" SG CYS R 488 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 131 " - pdb=" SG CYS N 166 " 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 BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG A 2 " - " BMA A 3 " NAG-ASN " NAG A 1 " - " ASN N 165 " Time building additional restraints: 0.43 Conformation dependent library (CDL) restraints added in 169.6 milliseconds 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1066 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 11 sheets defined 9.4% alpha, 26.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'R' and resid 337 through 343 Processing helix chain 'R' and resid 349 through 353 removed outlier: 3.533A pdb=" N TRP R 353 " --> pdb=" O VAL R 350 " (cutoff:3.500A) Processing helix chain 'R' and resid 365 through 370 Processing helix chain 'R' and resid 383 through 390 removed outlier: 4.456A pdb=" N ASN R 388 " --> pdb=" O THR R 385 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU R 390 " --> pdb=" O LEU R 387 " (cutoff:3.500A) Processing helix chain 'R' and resid 406 through 410 Processing helix chain 'R' and resid 416 through 422 Processing helix chain 'R' and resid 438 through 443 Processing helix chain 'R' and resid 502 through 506 Processing helix chain 'H' and resid 28 through 32 Processing sheet with id=AA1, first strand: chain 'R' and resid 354 through 358 removed outlier: 4.287A pdb=" N ASN R 394 " --> pdb=" O GLU R 516 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU R 516 " --> pdb=" O ASN R 394 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY R 431 " --> pdb=" O TYR R 380 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TYR R 380 " --> pdb=" O GLY R 431 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL R 433 " --> pdb=" O LYS R 378 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS R 378 " --> pdb=" O VAL R 433 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'L' and resid 5 through 6 removed outlier: 3.535A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 45 through 46 removed outlier: 3.577A pdb=" N GLN L 89 " --> pdb=" O ALA L 34 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 5 through 7 removed outlier: 3.598A pdb=" N VAL H 5 " --> pdb=" O ALA H 23 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 5 through 7 removed outlier: 3.598A pdb=" N VAL H 5 " --> pdb=" O ALA H 23 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 45 through 51 removed outlier: 6.750A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N SER H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N MET H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 29 through 31 Processing sheet with id=AA9, first strand: chain 'N' and resid 50 through 51 removed outlier: 4.109A pdb=" N ASP N 287 " --> pdb=" O LYS N 278 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 84 through 85 removed outlier: 3.547A pdb=" N SER N 172 " --> pdb=" O VAL N 126 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 224 through 229 removed outlier: 5.988A pdb=" N SER N 205 " --> pdb=" O PRO N 225 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL N 227 " --> pdb=" O ILE N 203 " (cutoff:3.500A) 128 hydrogen bonds defined for protein. 303 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: 0.62 Time building geometry restraints manager: 0.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.25: 730 1.25 - 1.40: 1345 1.40 - 1.55: 2650 1.55 - 1.70: 1 1.70 - 1.84: 23 Bond restraints: 4749 Sorted by residual: bond pdb=" CG PRO R 507 " pdb=" CD PRO R 507 " ideal model delta sigma weight residual 1.503 1.107 0.396 3.40e-02 8.65e+02 1.36e+02 bond pdb=" CB PRO R 507 " pdb=" CG PRO R 507 " ideal model delta sigma weight residual 1.492 1.155 0.337 5.00e-02 4.00e+02 4.54e+01 bond pdb=" N PRO R 507 " pdb=" CD PRO R 507 " ideal model delta sigma weight residual 1.473 1.507 -0.034 1.40e-02 5.10e+03 5.80e+00 bond pdb=" C1 BMA A 3 " pdb=" C2 BMA A 3 " ideal model delta sigma weight residual 1.519 1.553 -0.034 2.00e-02 2.50e+03 2.82e+00 bond pdb=" N PRO R 507 " pdb=" CA PRO R 507 " ideal model delta sigma weight residual 1.467 1.486 -0.019 1.21e-02 6.83e+03 2.55e+00 ... (remaining 4744 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.20: 6441 9.20 - 18.40: 0 18.40 - 27.60: 2 27.60 - 36.80: 0 36.80 - 46.00: 1 Bond angle restraints: 6444 Sorted by residual: angle pdb=" N PRO R 507 " pdb=" CD PRO R 507 " pdb=" CG PRO R 507 " ideal model delta sigma weight residual 103.20 76.09 27.11 1.50e+00 4.44e-01 3.27e+02 angle pdb=" CB PRO R 507 " pdb=" CG PRO R 507 " pdb=" CD PRO R 507 " ideal model delta sigma weight residual 106.10 152.10 -46.00 3.20e+00 9.77e-02 2.07e+02 angle pdb=" CA PRO R 507 " pdb=" CB PRO R 507 " pdb=" CG PRO R 507 " ideal model delta sigma weight residual 104.50 79.51 24.99 1.90e+00 2.77e-01 1.73e+02 angle pdb=" CA PRO R 507 " pdb=" N PRO R 507 " pdb=" CD PRO R 507 " ideal model delta sigma weight residual 112.00 102.91 9.09 1.40e+00 5.10e-01 4.22e+01 angle pdb=" C ASN N 165 " pdb=" CA ASN N 165 " pdb=" CB ASN N 165 " ideal model delta sigma weight residual 117.23 110.39 6.84 1.36e+00 5.41e-01 2.53e+01 ... (remaining 6439 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.06: 2408 15.06 - 30.12: 241 30.12 - 45.18: 63 45.18 - 60.24: 10 60.24 - 75.30: 10 Dihedral angle restraints: 2732 sinusoidal: 1059 harmonic: 1673 Sorted by residual: dihedral pdb=" CA PHE L 94 " pdb=" C PHE L 94 " pdb=" N PRO L 95 " pdb=" CA PRO L 95 " ideal model delta harmonic sigma weight residual 180.00 134.96 45.04 0 5.00e+00 4.00e-02 8.12e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual 93.00 164.63 -71.63 1 1.00e+01 1.00e-02 6.57e+01 dihedral pdb=" CA SER L 7 " pdb=" C SER L 7 " pdb=" N PRO L 8 " pdb=" CA PRO L 8 " ideal model delta harmonic sigma weight residual 180.00 140.26 39.74 0 5.00e+00 4.00e-02 6.32e+01 ... (remaining 2729 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 584 0.054 - 0.109: 90 0.109 - 0.163: 21 0.163 - 0.217: 1 0.217 - 0.272: 1 Chirality restraints: 697 Sorted by residual: chirality pdb=" C5 BMA A 3 " pdb=" C4 BMA A 3 " pdb=" C6 BMA A 3 " pdb=" O5 BMA A 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CA CYS N 166 " pdb=" N CYS N 166 " pdb=" C CYS N 166 " pdb=" CB CYS N 166 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.53e-01 chirality pdb=" CB VAL H 64 " pdb=" CA VAL H 64 " pdb=" CG1 VAL H 64 " pdb=" CG2 VAL H 64 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.66e-01 ... (remaining 694 not shown) Planarity restraints: 820 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN R 506 " 0.057 5.00e-02 4.00e+02 7.98e-02 1.02e+01 pdb=" N PRO R 507 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO R 507 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO R 507 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR N 38 " 0.047 5.00e-02 4.00e+02 7.17e-02 8.23e+00 pdb=" N PRO N 39 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO N 39 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO N 39 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE L 94 " -0.044 5.00e-02 4.00e+02 6.70e-02 7.19e+00 pdb=" N PRO L 95 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO L 95 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO L 95 " -0.037 5.00e-02 4.00e+02 ... (remaining 817 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 122 2.69 - 3.24: 4233 3.24 - 3.80: 6527 3.80 - 4.35: 8655 4.35 - 4.90: 14738 Nonbonded interactions: 34275 Sorted by model distance: nonbonded pdb=" OD1 ASP N 40 " pdb=" OH TYR N 204 " model vdw 2.142 3.040 nonbonded pdb=" O ASN R 439 " pdb=" OG SER R 443 " model vdw 2.187 3.040 nonbonded pdb=" O GLN H 3 " pdb=" OG SER H 25 " model vdw 2.195 3.040 nonbonded pdb=" OD1 ASN R 439 " pdb=" OG SER R 443 " model vdw 2.211 3.040 nonbonded pdb=" OH TYR N 91 " pdb=" OE1 GLU N 191 " model vdw 2.232 3.040 ... (remaining 34270 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: 6.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.390 Find NCS groups from input model: 0.020 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: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 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 : 0.008 0.396 4758 Z= 0.238 Angle : 1.013 46.004 6465 Z= 0.498 Chirality : 0.043 0.272 697 Planarity : 0.006 0.080 819 Dihedral : 13.465 75.298 1648 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.58 % Favored : 92.24 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.30 (0.35), residues: 554 helix: -2.80 (0.87), residues: 25 sheet: -0.56 (0.40), residues: 186 loop : -2.09 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 355 TYR 0.023 0.001 TYR H 102 PHE 0.013 0.001 PHE R 456 TRP 0.008 0.001 TRP L 35 HIS 0.001 0.000 HIS H 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00798 / 0.24 ( 4749) covalent geometry : angle 1.00534 / 0.50 ( 6444) SS BOND : bond 0.00673 / 0.33 ( 6) SS BOND : angle 1.40206 / 1.25 ( 12) hydrogen bonds : bond 0.27208 / 16.64 ( 123) hydrogen bonds : angle 10.14844 / 7.09 ( 303) link_BETA1-4 : bond 0.01091 / 0.57 ( 2) link_BETA1-4 : angle 2.47138 / 2.25 ( 6) link_NAG-ASN : bond 0.00072 / 0.04 ( 1) link_NAG-ASN : angle 4.33599 / 2.56 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.172 Fit side-chains REVERT: R 438 SER cc_start: 0.8217 (p) cc_final: 0.7686 (p) REVERT: H 83 MET cc_start: 0.6305 (ptt) cc_final: 0.6073 (ptt) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.0589 time to fit residues: 9.0866 Evaluate side-chains 94 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 54 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 498 GLN H 3 GLN H 35 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.156035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.134990 restraints weight = 6598.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.137704 restraints weight = 9928.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.137497 restraints weight = 5291.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.137420 restraints weight = 5367.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.138105 restraints weight = 4019.764| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 4758 Z= 0.234 Angle : 0.736 9.730 6465 Z= 0.392 Chirality : 0.047 0.209 697 Planarity : 0.007 0.073 819 Dihedral : 5.487 48.647 633 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.93 % Favored : 89.89 % Rotamer: Outliers : 1.59 % Allowed : 11.95 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.32 (0.35), residues: 554 helix: -2.85 (1.03), residues: 19 sheet: -0.58 (0.40), residues: 182 loop : -2.11 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 100 TYR 0.023 0.002 TYR H 95 PHE 0.030 0.002 PHE N 43 TRP 0.012 0.002 TRP L 35 HIS 0.003 0.001 HIS H 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00558 / 0.23 ( 4749) covalent geometry : angle 0.72625 / 0.39 ( 6444) SS BOND : bond 0.00802 / 0.44 ( 6) SS BOND : angle 2.02592 / 1.48 ( 12) hydrogen bonds : bond 0.04954 / 3.26 ( 123) hydrogen bonds : angle 7.11924 / 4.97 ( 303) link_BETA1-4 : bond 0.00528 / 0.28 ( 2) link_BETA1-4 : angle 1.85595 / 1.46 ( 6) link_NAG-ASN : bond 0.00293 / 0.15 ( 1) link_NAG-ASN : angle 3.13769 / 1.77 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.206 Fit side-chains REVERT: R 418 ILE cc_start: 0.9049 (tt) cc_final: 0.8769 (tt) REVERT: R 438 SER cc_start: 0.8039 (p) cc_final: 0.7442 (p) REVERT: R 498 GLN cc_start: 0.7808 (mt0) cc_final: 0.7603 (mt0) outliers start: 8 outliers final: 6 residues processed: 102 average time/residue: 0.0613 time to fit residues: 8.2679 Evaluate side-chains 96 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 90 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 468 ILE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain N residue 130 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 41 optimal weight: 0.3980 chunk 19 optimal weight: 0.6980 chunk 40 optimal weight: 0.2980 chunk 11 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 54 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN 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 = 0.157909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.135355 restraints weight = 6547.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.136967 restraints weight = 9054.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.138592 restraints weight = 7843.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.139293 restraints weight = 5308.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.139630 restraints weight = 5639.543| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4758 Z= 0.134 Angle : 0.642 9.477 6465 Z= 0.335 Chirality : 0.044 0.194 697 Planarity : 0.006 0.067 819 Dihedral : 5.263 47.063 633 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.86 % Favored : 92.96 % Rotamer: Outliers : 1.39 % Allowed : 15.74 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.15 (0.36), residues: 554 helix: -2.79 (1.12), residues: 19 sheet: -0.37 (0.40), residues: 188 loop : -2.07 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 19 TYR 0.012 0.001 TYR H 95 PHE 0.033 0.002 PHE R 456 TRP 0.007 0.001 TRP R 353 HIS 0.002 0.000 HIS H 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 ( 4749) covalent geometry : angle 0.63414 / 0.33 ( 6444) SS BOND : bond 0.00660 / 0.35 ( 6) SS BOND : angle 1.62760 / 1.21 ( 12) hydrogen bonds : bond 0.04010 / 2.63 ( 123) hydrogen bonds : angle 6.48654 / 4.53 ( 303) link_BETA1-4 : bond 0.00573 / 0.29 ( 2) link_BETA1-4 : angle 1.78615 / 1.52 ( 6) link_NAG-ASN : bond 0.00007 / 0.00 ( 1) link_NAG-ASN : angle 2.87019 / 1.62 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 99 time to evaluate : 0.121 Fit side-chains REVERT: R 418 ILE cc_start: 0.9138 (tt) cc_final: 0.8852 (tt) REVERT: R 438 SER cc_start: 0.8081 (p) cc_final: 0.7581 (p) REVERT: N 169 GLU cc_start: 0.7472 (mp0) cc_final: 0.6948 (mp0) outliers start: 7 outliers final: 5 residues processed: 104 average time/residue: 0.0610 time to fit residues: 8.2649 Evaluate side-chains 98 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 93 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 130 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 16 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 8 optimal weight: 0.1980 chunk 42 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 chunk 27 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 498 GLN H 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.159072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.135892 restraints weight = 6547.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.138736 restraints weight = 9374.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.139777 restraints weight = 5153.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.139352 restraints weight = 5259.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.140095 restraints weight = 4179.596| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4758 Z= 0.140 Angle : 0.632 9.102 6465 Z= 0.329 Chirality : 0.043 0.180 697 Planarity : 0.006 0.069 819 Dihedral : 5.210 46.839 633 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.76 % Favored : 92.06 % Rotamer: Outliers : 2.19 % Allowed : 16.14 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.36), residues: 554 helix: -2.62 (1.15), residues: 19 sheet: -0.49 (0.39), residues: 199 loop : -2.01 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 19 TYR 0.013 0.001 TYR H 95 PHE 0.024 0.002 PHE N 43 TRP 0.008 0.001 TRP R 353 HIS 0.002 0.000 HIS H 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 ( 4749) covalent geometry : angle 0.62459 / 0.33 ( 6444) SS BOND : bond 0.00575 / 0.31 ( 6) SS BOND : angle 1.46347 / 1.13 ( 12) hydrogen bonds : bond 0.03774 / 2.46 ( 123) hydrogen bonds : angle 6.17479 / 4.32 ( 303) link_BETA1-4 : bond 0.00497 / 0.26 ( 2) link_BETA1-4 : angle 1.75082 / 1.46 ( 6) link_NAG-ASN : bond 0.00035 / 0.02 ( 1) link_NAG-ASN : angle 2.84508 / 1.62 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.171 Fit side-chains REVERT: R 418 ILE cc_start: 0.9175 (tt) cc_final: 0.8956 (tt) REVERT: R 438 SER cc_start: 0.8135 (p) cc_final: 0.7585 (p) REVERT: N 169 GLU cc_start: 0.7489 (mp0) cc_final: 0.6990 (mp0) outliers start: 11 outliers final: 10 residues processed: 100 average time/residue: 0.0627 time to fit residues: 8.1878 Evaluate side-chains 101 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 468 ILE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain N residue 29 THR Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 166 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 30 optimal weight: 0.1980 chunk 36 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 10 optimal weight: 0.1980 chunk 9 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 498 GLN H 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.176070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.150025 restraints weight = 6498.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.151434 restraints weight = 7703.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.153627 restraints weight = 6365.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.153999 restraints weight = 4363.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.154430 restraints weight = 4886.897| |-----------------------------------------------------------------------------| r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4758 Z= 0.132 Angle : 0.641 10.932 6465 Z= 0.328 Chirality : 0.043 0.185 697 Planarity : 0.005 0.067 819 Dihedral : 5.205 46.639 633 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.22 % Favored : 92.60 % Rotamer: Outliers : 3.39 % Allowed : 16.33 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.36), residues: 554 helix: -2.44 (1.13), residues: 19 sheet: -0.42 (0.38), residues: 202 loop : -2.02 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 19 TYR 0.013 0.001 TYR H 95 PHE 0.037 0.002 PHE R 456 TRP 0.008 0.001 TRP R 353 HIS 0.002 0.000 HIS H 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 ( 4749) covalent geometry : angle 0.63426 / 0.33 ( 6444) SS BOND : bond 0.00549 / 0.30 ( 6) SS BOND : angle 1.44437 / 1.12 ( 12) hydrogen bonds : bond 0.03572 / 2.35 ( 123) hydrogen bonds : angle 5.95900 / 4.20 ( 303) link_BETA1-4 : bond 0.00691 / 0.35 ( 2) link_BETA1-4 : angle 1.73690 / 1.47 ( 6) link_NAG-ASN : bond 0.00012 / 0.01 ( 1) link_NAG-ASN : angle 2.82959 / 1.62 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.170 Fit side-chains REVERT: R 438 SER cc_start: 0.7871 (p) cc_final: 0.7330 (p) REVERT: H 121 GLN cc_start: 0.6629 (OUTLIER) cc_final: 0.5724 (pm20) REVERT: N 32 PHE cc_start: 0.8204 (p90) cc_final: 0.8001 (p90) REVERT: N 169 GLU cc_start: 0.7540 (mp0) cc_final: 0.6989 (mp0) outliers start: 17 outliers final: 11 residues processed: 106 average time/residue: 0.0617 time to fit residues: 8.6471 Evaluate side-chains 103 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 468 ILE Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain H residue 121 GLN Chi-restraints excluded: chain N residue 29 THR Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 166 CYS Chi-restraints excluded: chain N residue 274 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 44 optimal weight: 0.1980 chunk 30 optimal weight: 0.0870 chunk 46 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 43 optimal weight: 0.0870 chunk 34 optimal weight: 0.6980 chunk 28 optimal weight: 0.2980 chunk 15 optimal weight: 0.1980 chunk 22 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.1736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 437 ASN R 498 GLN H 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.180110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.153268 restraints weight = 6593.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.156535 restraints weight = 7046.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.157507 restraints weight = 5936.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.158608 restraints weight = 3956.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.159186 restraints weight = 3692.286| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 4758 Z= 0.096 Angle : 0.607 8.938 6465 Z= 0.309 Chirality : 0.043 0.200 697 Planarity : 0.005 0.066 819 Dihedral : 4.973 44.512 633 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.96 % Favored : 93.86 % Rotamer: Outliers : 2.59 % Allowed : 16.73 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.36), residues: 554 helix: -2.19 (1.17), residues: 19 sheet: -0.32 (0.38), residues: 207 loop : -1.92 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 19 TYR 0.013 0.001 TYR R 380 PHE 0.020 0.001 PHE N 43 TRP 0.005 0.001 TRP R 436 HIS 0.001 0.000 HIS L 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 ( 4749) covalent geometry : angle 0.59958 / 0.31 ( 6444) SS BOND : bond 0.00378 / 0.20 ( 6) SS BOND : angle 1.60309 / 1.45 ( 12) hydrogen bonds : bond 0.03013 / 1.96 ( 123) hydrogen bonds : angle 5.68583 / 4.02 ( 303) link_BETA1-4 : bond 0.00505 / 0.26 ( 2) link_BETA1-4 : angle 1.65340 / 1.44 ( 6) link_NAG-ASN : bond 0.00133 / 0.07 ( 1) link_NAG-ASN : angle 2.63898 / 1.53 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.170 Fit side-chains REVERT: R 438 SER cc_start: 0.7770 (p) cc_final: 0.7249 (p) REVERT: L 36 TYR cc_start: 0.8792 (m-80) cc_final: 0.8557 (m-80) REVERT: N 32 PHE cc_start: 0.8192 (p90) cc_final: 0.7863 (p90) REVERT: N 132 GLU cc_start: 0.6997 (mm-30) cc_final: 0.6731 (mm-30) REVERT: N 169 GLU cc_start: 0.7564 (mp0) cc_final: 0.6955 (mp0) outliers start: 13 outliers final: 12 residues processed: 109 average time/residue: 0.0586 time to fit residues: 8.5414 Evaluate side-chains 109 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 437 ASN Chi-restraints excluded: chain R residue 468 ILE Chi-restraints excluded: chain R residue 508 TYR Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain N residue 29 THR Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 166 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 29 optimal weight: 0.2980 chunk 2 optimal weight: 0.8980 chunk 15 optimal weight: 0.0980 chunk 53 optimal weight: 2.9990 chunk 9 optimal weight: 0.3980 chunk 32 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 28 optimal weight: 0.0070 chunk 25 optimal weight: 3.9990 chunk 51 optimal weight: 0.1980 chunk 44 optimal weight: 0.7980 overall best weight: 0.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 498 GLN H 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.180526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.155157 restraints weight = 6540.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.156018 restraints weight = 7110.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.157823 restraints weight = 6909.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.158859 restraints weight = 4366.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.159413 restraints weight = 4195.312| |-----------------------------------------------------------------------------| r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4758 Z= 0.097 Angle : 0.607 11.129 6465 Z= 0.307 Chirality : 0.043 0.176 697 Planarity : 0.005 0.066 819 Dihedral : 4.901 44.087 633 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.50 % Favored : 93.32 % Rotamer: Outliers : 2.39 % Allowed : 17.33 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.36), residues: 554 helix: -2.12 (1.16), residues: 19 sheet: -0.28 (0.38), residues: 207 loop : -1.92 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 19 TYR 0.013 0.001 TYR R 380 PHE 0.020 0.001 PHE N 43 TRP 0.004 0.001 TRP H 47 HIS 0.001 0.000 HIS H 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 ( 4749) covalent geometry : angle 0.60136 / 0.31 ( 6444) SS BOND : bond 0.00559 / 0.28 ( 6) SS BOND : angle 1.28462 / 1.11 ( 12) hydrogen bonds : bond 0.02840 / 1.84 ( 123) hydrogen bonds : angle 5.55416 / 3.94 ( 303) link_BETA1-4 : bond 0.00548 / 0.28 ( 2) link_BETA1-4 : angle 1.58380 / 1.37 ( 6) link_NAG-ASN : bond 0.00094 / 0.05 ( 1) link_NAG-ASN : angle 2.59656 / 1.49 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.188 Fit side-chains REVERT: R 438 SER cc_start: 0.7888 (p) cc_final: 0.7406 (p) REVERT: L 36 TYR cc_start: 0.8779 (m-80) cc_final: 0.8535 (m-80) REVERT: N 32 PHE cc_start: 0.8129 (p90) cc_final: 0.7818 (p90) REVERT: N 132 GLU cc_start: 0.6999 (mm-30) cc_final: 0.6742 (mm-30) REVERT: N 169 GLU cc_start: 0.7534 (mp0) cc_final: 0.6929 (mp0) outliers start: 12 outliers final: 12 residues processed: 107 average time/residue: 0.0632 time to fit residues: 8.9294 Evaluate side-chains 108 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 468 ILE Chi-restraints excluded: chain R residue 508 TYR Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain N residue 29 THR Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 166 CYS Chi-restraints excluded: chain N residue 274 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 15 optimal weight: 0.0000 chunk 41 optimal weight: 0.9980 chunk 44 optimal weight: 0.1980 chunk 26 optimal weight: 0.8980 chunk 54 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 40 optimal weight: 0.0470 chunk 52 optimal weight: 0.6980 overall best weight: 0.2882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 437 ASN R 498 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.163617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.139061 restraints weight = 6540.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.141128 restraints weight = 8982.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.143547 restraints weight = 6622.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.143427 restraints weight = 4621.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.144385 restraints weight = 4079.951| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4758 Z= 0.102 Angle : 0.611 12.314 6465 Z= 0.308 Chirality : 0.043 0.175 697 Planarity : 0.006 0.073 819 Dihedral : 4.901 45.261 633 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.32 % Favored : 93.50 % Rotamer: Outliers : 3.39 % Allowed : 17.73 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.36), residues: 554 helix: -2.30 (1.13), residues: 20 sheet: -0.23 (0.38), residues: 206 loop : -1.95 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 19 TYR 0.011 0.001 TYR R 473 PHE 0.020 0.001 PHE N 43 TRP 0.008 0.001 TRP R 436 HIS 0.001 0.000 HIS H 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 ( 4749) covalent geometry : angle 0.60564 / 0.31 ( 6444) SS BOND : bond 0.00528 / 0.27 ( 6) SS BOND : angle 1.25383 / 1.07 ( 12) hydrogen bonds : bond 0.02997 / 1.93 ( 123) hydrogen bonds : angle 5.35737 / 3.79 ( 303) link_BETA1-4 : bond 0.00554 / 0.28 ( 2) link_BETA1-4 : angle 1.53722 / 1.32 ( 6) link_NAG-ASN : bond 0.00052 / 0.03 ( 1) link_NAG-ASN : angle 2.59482 / 1.48 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.166 Fit side-chains REVERT: R 438 SER cc_start: 0.7769 (p) cc_final: 0.7293 (p) REVERT: L 36 TYR cc_start: 0.8753 (m-80) cc_final: 0.8513 (m-80) REVERT: H 121 GLN cc_start: 0.6472 (OUTLIER) cc_final: 0.5846 (pm20) REVERT: N 132 GLU cc_start: 0.6961 (mm-30) cc_final: 0.6708 (mm-30) REVERT: N 169 GLU cc_start: 0.7518 (mp0) cc_final: 0.6915 (mp0) outliers start: 17 outliers final: 13 residues processed: 107 average time/residue: 0.0542 time to fit residues: 7.8698 Evaluate side-chains 106 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 437 ASN Chi-restraints excluded: chain R residue 508 TYR Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 121 GLN Chi-restraints excluded: chain N residue 29 THR Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 166 CYS Chi-restraints excluded: chain N residue 274 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 35 optimal weight: 0.0470 chunk 7 optimal weight: 2.9990 chunk 34 optimal weight: 0.4980 chunk 31 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 44 optimal weight: 0.0000 chunk 29 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 overall best weight: 0.4082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 437 ASN R 498 GLN H 3 GLN H 59 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.162666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.138130 restraints weight = 6434.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.141444 restraints weight = 9824.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.143118 restraints weight = 6377.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.142959 restraints weight = 4606.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.143669 restraints weight = 4520.939| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4758 Z= 0.116 Angle : 0.628 13.174 6465 Z= 0.317 Chirality : 0.043 0.175 697 Planarity : 0.006 0.067 819 Dihedral : 4.894 44.110 633 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.86 % Favored : 92.96 % Rotamer: Outliers : 3.59 % Allowed : 17.13 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.36), residues: 554 helix: -2.29 (1.12), residues: 20 sheet: -0.15 (0.38), residues: 206 loop : -1.96 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 19 TYR 0.012 0.001 TYR H 95 PHE 0.042 0.001 PHE R 429 TRP 0.007 0.001 TRP R 436 HIS 0.002 0.000 HIS H 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 4749) covalent geometry : angle 0.62215 / 0.32 ( 6444) SS BOND : bond 0.00521 / 0.27 ( 6) SS BOND : angle 1.30221 / 1.11 ( 12) hydrogen bonds : bond 0.03028 / 1.95 ( 123) hydrogen bonds : angle 5.33371 / 3.76 ( 303) link_BETA1-4 : bond 0.00648 / 0.33 ( 2) link_BETA1-4 : angle 1.52891 / 1.31 ( 6) link_NAG-ASN : bond 0.00004 / 0.00 ( 1) link_NAG-ASN : angle 2.59495 / 1.47 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.170 Fit side-chains REVERT: R 438 SER cc_start: 0.7403 (p) cc_final: 0.6992 (p) REVERT: H 121 GLN cc_start: 0.6500 (OUTLIER) cc_final: 0.5868 (pm20) REVERT: N 132 GLU cc_start: 0.6981 (mm-30) cc_final: 0.6745 (mm-30) REVERT: N 169 GLU cc_start: 0.7561 (mp0) cc_final: 0.6962 (mp0) outliers start: 18 outliers final: 15 residues processed: 106 average time/residue: 0.0556 time to fit residues: 8.0699 Evaluate side-chains 107 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 437 ASN Chi-restraints excluded: chain R residue 498 GLN Chi-restraints excluded: chain R residue 508 TYR Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 91 TYR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 121 GLN Chi-restraints excluded: chain N residue 29 THR Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 166 CYS Chi-restraints excluded: chain N residue 274 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 50 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 36 optimal weight: 0.2980 chunk 34 optimal weight: 0.4980 chunk 29 optimal weight: 0.0980 chunk 43 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 437 ASN R 498 GLN L 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.160588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.137366 restraints weight = 6575.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.140254 restraints weight = 9080.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.140819 restraints weight = 4826.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.140554 restraints weight = 4625.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.140885 restraints weight = 3739.650| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4758 Z= 0.157 Angle : 0.672 12.862 6465 Z= 0.338 Chirality : 0.046 0.346 697 Planarity : 0.006 0.067 819 Dihedral : 5.006 45.039 633 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.04 % Favored : 92.78 % Rotamer: Outliers : 3.39 % Allowed : 17.53 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.37), residues: 554 helix: -2.09 (1.16), residues: 19 sheet: -0.17 (0.39), residues: 207 loop : -1.94 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 19 TYR 0.017 0.001 TYR H 95 PHE 0.055 0.002 PHE R 429 TRP 0.008 0.001 TRP R 436 HIS 0.000 0.000 HIS H 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 ( 4749) covalent geometry : angle 0.66595 / 0.34 ( 6444) SS BOND : bond 0.00551 / 0.29 ( 6) SS BOND : angle 1.35394 / 1.13 ( 12) hydrogen bonds : bond 0.03286 / 2.13 ( 123) hydrogen bonds : angle 5.36724 / 3.79 ( 303) link_BETA1-4 : bond 0.00589 / 0.30 ( 2) link_BETA1-4 : angle 1.55313 / 1.30 ( 6) link_NAG-ASN : bond 0.00098 / 0.05 ( 1) link_NAG-ASN : angle 2.64279 / 1.49 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.165 Fit side-chains REVERT: R 438 SER cc_start: 0.7789 (p) cc_final: 0.7277 (p) REVERT: H 121 GLN cc_start: 0.6539 (OUTLIER) cc_final: 0.5898 (pm20) REVERT: N 132 GLU cc_start: 0.7011 (mm-30) cc_final: 0.6753 (mm-30) REVERT: N 169 GLU cc_start: 0.7550 (mp0) cc_final: 0.6909 (mp0) outliers start: 17 outliers final: 14 residues processed: 103 average time/residue: 0.0553 time to fit residues: 7.7538 Evaluate side-chains 108 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 437 ASN Chi-restraints excluded: chain R residue 508 TYR Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 91 TYR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 121 GLN Chi-restraints excluded: chain N residue 29 THR Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 166 CYS Chi-restraints excluded: chain N residue 274 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 33 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 36 optimal weight: 0.0570 chunk 6 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 15 optimal weight: 0.4980 chunk 55 optimal weight: 0.7980 chunk 9 optimal weight: 0.0980 overall best weight: 0.3898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 437 ASN R 498 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.161440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.136909 restraints weight = 6594.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.139625 restraints weight = 9361.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.141947 restraints weight = 6332.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.141926 restraints weight = 4851.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.142539 restraints weight = 4520.293| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4758 Z= 0.115 Angle : 0.645 12.745 6465 Z= 0.325 Chirality : 0.044 0.228 697 Planarity : 0.006 0.066 819 Dihedral : 4.964 44.493 633 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.86 % Favored : 92.96 % Rotamer: Outliers : 3.19 % Allowed : 17.33 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.37), residues: 554 helix: -2.63 (0.91), residues: 27 sheet: -0.05 (0.39), residues: 204 loop : -1.95 (0.35), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 19 TYR 0.012 0.001 TYR H 95 PHE 0.050 0.002 PHE R 429 TRP 0.008 0.001 TRP R 436 HIS 0.000 0.000 HIS H 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.11 ( 4749) covalent geometry : angle 0.63963 / 0.32 ( 6444) SS BOND : bond 0.00561 / 0.29 ( 6) SS BOND : angle 1.31023 / 1.11 ( 12) hydrogen bonds : bond 0.03031 / 1.98 ( 123) hydrogen bonds : angle 5.34749 / 3.77 ( 303) link_BETA1-4 : bond 0.00585 / 0.30 ( 2) link_BETA1-4 : angle 1.58071 / 1.35 ( 6) link_NAG-ASN : bond 0.00067 / 0.04 ( 1) link_NAG-ASN : angle 2.65037 / 1.50 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1025.33 seconds wall clock time: 18 minutes 26.04 seconds (1106.04 seconds total)