Starting phenix.real_space_refine on Wed Jul 1 22:05:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ru8_24699/07_2026/7ru8_24699.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ru8_24699/07_2026/7ru8_24699.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7ru8_24699/07_2026/7ru8_24699.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ru8_24699/07_2026/7ru8_24699.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ru8_24699/07_2026/7ru8_24699.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ru8_24699/07_2026/7ru8_24699.map" model { file = "/net/cci-nas-00/data/ceres_data/7ru8_24699/07_2026/7ru8_24699.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ru8_24699/07_2026/7ru8_24699.cif" } resolution = 3.8 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= -0.001 sd= 0.014 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 15 5.16 5 C 2031 2.51 5 N 532 2.21 5 O 620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 3198 Number of models: 1 Model: "" Number of chains: 5 Chain: "H" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 956 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "L" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 812 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "C" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1388 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 9, 'TRANS': 164} Chain breaks: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" 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 chiralities: 1 Time building chain proxies: 0.60, per 1000 atoms: 0.19 Number of scatterers: 3198 At special positions: 0 Unit cell: (56.65, 75.19, 107.12, 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 15 16.00 O 620 8.00 N 532 7.00 C 2031 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 99 " - pdb=" SG CYS H 100D" distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.02 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-ASN " NAG A 1 " - " ASN C 343 " " NAG L 201 " - " ASN L 28 " Time building additional restraints: 0.17 Conformation dependent library (CDL) restraints added in 71.4 milliseconds 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 742 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 8 sheets defined 11.4% alpha, 28.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.494A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 58 through 59 removed outlier: 5.550A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 96 through 100 Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.826A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.584A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 354 through 357 Processing sheet with id=AA8, first strand: chain 'C' and resid 452 through 454 108 hydrogen bonds defined for protein. 249 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: 0.28 Time building geometry restraints manager: 0.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 623 1.32 - 1.45: 1156 1.45 - 1.59: 1469 1.59 - 1.73: 10 1.73 - 1.87: 17 Bond restraints: 3275 Sorted by residual: bond pdb=" CB LEU C 387 " pdb=" CG LEU C 387 " ideal model delta sigma weight residual 1.530 1.634 -0.104 2.00e-02 2.50e+03 2.72e+01 bond pdb=" CG PHE C 515 " pdb=" CD2 PHE C 515 " ideal model delta sigma weight residual 1.384 1.489 -0.105 2.10e-02 2.27e+03 2.51e+01 bond pdb=" CD ARG L 96 " pdb=" NE ARG L 96 " ideal model delta sigma weight residual 1.458 1.390 0.068 1.40e-02 5.10e+03 2.37e+01 bond pdb=" CG PHE C 515 " pdb=" CD1 PHE C 515 " ideal model delta sigma weight residual 1.384 1.486 -0.102 2.10e-02 2.27e+03 2.36e+01 bond pdb=" CG PHE C 429 " pdb=" CD2 PHE C 429 " ideal model delta sigma weight residual 1.384 1.486 -0.102 2.10e-02 2.27e+03 2.34e+01 ... (remaining 3270 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 3844 2.57 - 5.14: 506 5.14 - 7.71: 78 7.71 - 10.27: 12 10.27 - 12.84: 3 Bond angle restraints: 4443 Sorted by residual: angle pdb=" N SER L 30 " pdb=" CA SER L 30 " pdb=" C SER L 30 " ideal model delta sigma weight residual 111.28 119.73 -8.45 1.09e+00 8.42e-01 6.01e+01 angle pdb=" C SER C 383 " pdb=" N PRO C 384 " pdb=" CA PRO C 384 " ideal model delta sigma weight residual 119.56 126.92 -7.36 1.01e+00 9.80e-01 5.31e+01 angle pdb=" N ARG H 94 " pdb=" CA ARG H 94 " pdb=" C ARG H 94 " ideal model delta sigma weight residual 113.17 122.27 -9.10 1.26e+00 6.30e-01 5.21e+01 angle pdb=" C ASN C 487 " pdb=" N CYS C 488 " pdb=" CA CYS C 488 " ideal model delta sigma weight residual 121.69 134.53 -12.84 1.85e+00 2.92e-01 4.82e+01 angle pdb=" N PRO H 41 " pdb=" CA PRO H 41 " pdb=" C PRO H 41 " ideal model delta sigma weight residual 111.26 100.42 10.84 1.63e+00 3.76e-01 4.42e+01 ... (remaining 4438 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.06: 1831 17.06 - 34.12: 44 34.12 - 51.19: 21 51.19 - 68.25: 7 68.25 - 85.31: 3 Dihedral angle restraints: 1906 sinusoidal: 736 harmonic: 1170 Sorted by residual: dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual 93.00 127.21 -34.21 1 1.00e+01 1.00e-02 1.66e+01 dihedral pdb=" N ILE H 31 " pdb=" C ILE H 31 " pdb=" CA ILE H 31 " pdb=" CB ILE H 31 " ideal model delta harmonic sigma weight residual 123.40 131.51 -8.11 0 2.50e+00 1.60e-01 1.05e+01 dihedral pdb=" C ARG L 96 " pdb=" N ARG L 96 " pdb=" CA ARG L 96 " pdb=" CB ARG L 96 " ideal model delta harmonic sigma weight residual -122.60 -114.72 -7.88 0 2.50e+00 1.60e-01 9.92e+00 ... (remaining 1903 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.103: 354 0.103 - 0.205: 97 0.205 - 0.307: 26 0.307 - 0.409: 4 0.409 - 0.511: 6 Chirality restraints: 487 Sorted by residual: chirality pdb=" C1 NAG A 2 " pdb=" O4 NAG A 1 " pdb=" C2 NAG A 2 " pdb=" O5 NAG A 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.51e+01 chirality pdb=" C1 NAG L 201 " pdb=" ND2 ASN L 28 " pdb=" C2 NAG L 201 " pdb=" O5 NAG L 201 " both_signs ideal model delta sigma weight residual False -2.40 -2.91 0.51 2.00e-01 2.50e+01 6.53e+00 chirality pdb=" CG LEU C 387 " pdb=" CB LEU C 387 " pdb=" CD1 LEU C 387 " pdb=" CD2 LEU C 387 " both_signs ideal model delta sigma weight residual False -2.59 -3.09 0.51 2.00e-01 2.50e+01 6.38e+00 ... (remaining 484 not shown) Planarity restraints: 567 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN L 28 " 0.061 2.00e-02 2.50e+03 6.58e-02 5.41e+01 pdb=" CG ASN L 28 " -0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN L 28 " -0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN L 28 " -0.105 2.00e-02 2.50e+03 pdb=" C1 NAG L 201 " 0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 489 " 0.086 2.00e-02 2.50e+03 4.50e-02 4.04e+01 pdb=" CG TYR C 489 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR C 489 " -0.041 2.00e-02 2.50e+03 pdb=" CD2 TYR C 489 " -0.031 2.00e-02 2.50e+03 pdb=" CE1 TYR C 489 " -0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR C 489 " -0.020 2.00e-02 2.50e+03 pdb=" CZ TYR C 489 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 489 " 0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 47 " -0.077 2.00e-02 2.50e+03 3.89e-02 3.79e+01 pdb=" CG TRP H 47 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TRP H 47 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP H 47 " 0.040 2.00e-02 2.50e+03 pdb=" NE1 TRP H 47 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 TRP H 47 " 0.009 2.00e-02 2.50e+03 pdb=" CE3 TRP H 47 " 0.057 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 47 " -0.034 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 47 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP H 47 " -0.049 2.00e-02 2.50e+03 ... (remaining 564 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.86: 1160 2.86 - 3.37: 2899 3.37 - 3.88: 5523 3.88 - 4.39: 6414 4.39 - 4.90: 10245 Nonbonded interactions: 26241 Sorted by model distance: nonbonded pdb=" N VAL C 350 " pdb=" O VAL C 350 " model vdw 2.356 2.496 nonbonded pdb=" C SER C 349 " pdb=" O VAL C 350 " model vdw 2.474 3.270 nonbonded pdb=" N TYR H 32 " pdb=" O TYR H 32 " model vdw 2.478 2.496 nonbonded pdb=" N PHE C 429 " pdb=" O PHE C 429 " model vdw 2.504 2.496 nonbonded pdb=" N ALA H 40 " pdb=" O ALA H 40 " model vdw 2.504 2.496 ... (remaining 26236 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: 5.270 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: 0.030 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 3.310 Find NCS groups from input model: 0.010 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:0.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 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 : 0.022 0.125 3284 Z= 1.133 Angle : 1.877 12.843 4464 Z= 1.222 Chirality : 0.116 0.511 487 Planarity : 0.009 0.045 565 Dihedral : 10.444 85.311 1146 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 1.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.23 (0.41), residues: 395 helix: -4.33 (0.37), residues: 21 sheet: 0.28 (0.44), residues: 134 loop : 0.10 (0.40), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 403 TYR 0.086 0.009 TYR C 489 PHE 0.033 0.007 PHE C 429 TRP 0.077 0.017 TRP H 47 Details of bonding type rmsd/Z covalent geometry : bond 0.02183 / 1.13 ( 3275) covalent geometry : angle 1.86675 / 1.22 ( 4443) SS BOND : bond 0.00837 / 0.38 ( 6) SS BOND : angle 2.72365 / 1.65 ( 12) hydrogen bonds : bond 0.16458 / 11.05 ( 104) hydrogen bonds : angle 9.49181 / 6.36 ( 249) link_BETA1-4 : bond 0.05856 / 3.08 ( 1) link_BETA1-4 : angle 4.64772 / 2.44 ( 3) link_NAG-ASN : bond 0.07511 / 3.79 ( 2) link_NAG-ASN : angle 4.05566 / 2.46 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 13 LYS cc_start: 0.2507 (mttt) cc_final: 0.1758 (mtpp) REVERT: L 2 ILE cc_start: 0.7216 (mt) cc_final: 0.6843 (mt) REVERT: C 424 LYS cc_start: 0.8357 (tptt) cc_final: 0.7692 (tptt) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.0711 time to fit residues: 8.1340 Evaluate side-chains 49 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 89 GLN C 501 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.082184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.076335 restraints weight = 14777.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.077890 restraints weight = 7816.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.078892 restraints weight = 4716.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.079535 restraints weight = 3111.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.079935 restraints weight = 2204.027| |-----------------------------------------------------------------------------| r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3284 Z= 0.191 Angle : 0.809 7.422 4464 Z= 0.431 Chirality : 0.047 0.138 487 Planarity : 0.005 0.042 565 Dihedral : 5.764 24.065 447 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 2.62 % Allowed : 11.92 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.43 (0.43), residues: 395 helix: -3.54 (0.78), residues: 21 sheet: 0.12 (0.46), residues: 146 loop : -0.13 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 96 TYR 0.024 0.002 TYR L 87 PHE 0.034 0.003 PHE L 71 TRP 0.034 0.003 TRP H 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.19 ( 3275) covalent geometry : angle 0.79738 / 0.43 ( 4443) SS BOND : bond 0.00882 / 0.44 ( 6) SS BOND : angle 1.54082 / 1.08 ( 12) hydrogen bonds : bond 0.04004 / 2.61 ( 104) hydrogen bonds : angle 7.41132 / 4.86 ( 249) link_BETA1-4 : bond 0.00028 / 0.01 ( 1) link_BETA1-4 : angle 1.44063 / 0.79 ( 3) link_NAG-ASN : bond 0.00212 / 0.11 ( 2) link_NAG-ASN : angle 3.25748 / 1.80 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 13 LYS cc_start: 0.3021 (mttt) cc_final: 0.2283 (tttm) REVERT: L 94 THR cc_start: 0.7197 (p) cc_final: 0.6953 (p) REVERT: C 353 TRP cc_start: 0.6389 (m-90) cc_final: 0.6025 (m-90) outliers start: 9 outliers final: 5 residues processed: 62 average time/residue: 0.0506 time to fit residues: 3.8470 Evaluate side-chains 50 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 503 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 22 optimal weight: 0.0050 chunk 14 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 1 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 481 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.079779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.073354 restraints weight = 14224.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.074990 restraints weight = 7639.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.076012 restraints weight = 4601.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.076654 restraints weight = 3050.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.077114 restraints weight = 2199.703| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.4483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3284 Z= 0.165 Angle : 0.710 6.276 4464 Z= 0.378 Chirality : 0.047 0.203 487 Planarity : 0.004 0.043 565 Dihedral : 5.398 19.365 447 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 2.62 % Allowed : 13.37 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.68 (0.43), residues: 395 helix: -2.76 (1.31), residues: 14 sheet: 0.06 (0.49), residues: 135 loop : -0.57 (0.39), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 403 TYR 0.019 0.002 TYR C 489 PHE 0.024 0.002 PHE C 429 TRP 0.029 0.002 TRP H 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 ( 3275) covalent geometry : angle 0.69930 / 0.38 ( 4443) SS BOND : bond 0.00400 / 0.25 ( 6) SS BOND : angle 1.67515 / 1.08 ( 12) hydrogen bonds : bond 0.03482 / 2.21 ( 104) hydrogen bonds : angle 6.60934 / 4.36 ( 249) link_BETA1-4 : bond 0.00126 / 0.07 ( 1) link_BETA1-4 : angle 1.27045 / 0.73 ( 3) link_NAG-ASN : bond 0.00141 / 0.07 ( 2) link_NAG-ASN : angle 2.58707 / 1.56 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.084 Fit side-chains revert: symmetry clash REVERT: C 353 TRP cc_start: 0.6433 (m-90) cc_final: 0.6188 (m-90) REVERT: C 387 LEU cc_start: 0.8168 (tp) cc_final: 0.7676 (tp) outliers start: 9 outliers final: 4 residues processed: 56 average time/residue: 0.0566 time to fit residues: 3.8690 Evaluate side-chains 49 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 503 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 25 optimal weight: 0.9980 chunk 4 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 1 GLN L 90 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.078581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.072230 restraints weight = 14204.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.073826 restraints weight = 7551.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.074814 restraints weight = 4531.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.075461 restraints weight = 2990.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.075861 restraints weight = 2126.753| |-----------------------------------------------------------------------------| r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.5063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3284 Z= 0.173 Angle : 0.684 6.153 4464 Z= 0.364 Chirality : 0.047 0.137 487 Planarity : 0.005 0.045 565 Dihedral : 5.366 22.728 447 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 2.91 % Allowed : 14.53 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.80 (0.43), residues: 395 helix: -2.87 (1.20), residues: 15 sheet: 0.10 (0.50), residues: 130 loop : -0.71 (0.38), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 403 TYR 0.013 0.002 TYR C 489 PHE 0.019 0.002 PHE L 71 TRP 0.031 0.002 TRP H 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 ( 3275) covalent geometry : angle 0.67861 / 0.36 ( 4443) SS BOND : bond 0.00333 / 0.20 ( 6) SS BOND : angle 0.73812 / 0.51 ( 12) hydrogen bonds : bond 0.03350 / 2.04 ( 104) hydrogen bonds : angle 6.44512 / 4.17 ( 249) link_BETA1-4 : bond 0.00099 / 0.05 ( 1) link_BETA1-4 : angle 1.06714 / 0.62 ( 3) link_NAG-ASN : bond 0.00119 / 0.06 ( 2) link_NAG-ASN : angle 2.42077 / 1.56 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 353 TRP cc_start: 0.6525 (m-90) cc_final: 0.6297 (m-90) REVERT: C 387 LEU cc_start: 0.8252 (tp) cc_final: 0.7892 (tp) outliers start: 10 outliers final: 8 residues processed: 51 average time/residue: 0.0390 time to fit residues: 2.5337 Evaluate side-chains 51 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 471 GLU Chi-restraints excluded: chain C residue 503 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 13 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 22 optimal weight: 0.0980 chunk 15 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 34 optimal weight: 0.0060 chunk 24 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 27 optimal weight: 0.1980 chunk 18 optimal weight: 0.8980 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.080196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.073925 restraints weight = 14085.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.075488 restraints weight = 7526.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.076441 restraints weight = 4549.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.077094 restraints weight = 3031.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.077480 restraints weight = 2153.042| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.5346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3284 Z= 0.127 Angle : 0.626 5.986 4464 Z= 0.331 Chirality : 0.045 0.134 487 Planarity : 0.004 0.047 565 Dihedral : 5.164 20.434 447 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 3.49 % Allowed : 14.53 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.73 (0.43), residues: 395 helix: -2.82 (1.19), residues: 15 sheet: 0.10 (0.49), residues: 130 loop : -0.64 (0.39), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 509 TYR 0.012 0.001 TYR C 351 PHE 0.016 0.001 PHE L 71 TRP 0.027 0.002 TRP H 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 ( 3275) covalent geometry : angle 0.62040 / 0.33 ( 4443) SS BOND : bond 0.00440 / 0.22 ( 6) SS BOND : angle 0.71884 / 0.43 ( 12) hydrogen bonds : bond 0.02923 / 1.76 ( 104) hydrogen bonds : angle 6.07142 / 3.93 ( 249) link_BETA1-4 : bond 0.00162 / 0.09 ( 1) link_BETA1-4 : angle 1.13326 / 0.66 ( 3) link_NAG-ASN : bond 0.00090 / 0.04 ( 2) link_NAG-ASN : angle 2.26818 / 1.54 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 71 PHE cc_start: 0.5256 (t80) cc_final: 0.4993 (m-80) REVERT: C 387 LEU cc_start: 0.8264 (tp) cc_final: 0.7924 (tp) REVERT: C 509 ARG cc_start: 0.8895 (OUTLIER) cc_final: 0.8535 (mtm-85) outliers start: 12 outliers final: 9 residues processed: 60 average time/residue: 0.0774 time to fit residues: 5.5730 Evaluate side-chains 56 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 509 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 26 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 36 optimal weight: 0.0970 chunk 1 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.078986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.072554 restraints weight = 13994.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.074187 restraints weight = 7263.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.075198 restraints weight = 4299.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.075843 restraints weight = 2820.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.076232 restraints weight = 2003.612| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.5591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3284 Z= 0.148 Angle : 0.634 5.976 4464 Z= 0.335 Chirality : 0.045 0.135 487 Planarity : 0.004 0.045 565 Dihedral : 5.048 20.897 447 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 2.91 % Allowed : 15.41 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.75 (0.43), residues: 395 helix: -2.93 (1.18), residues: 15 sheet: 0.24 (0.51), residues: 122 loop : -0.72 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 466 TYR 0.025 0.001 TYR L 92 PHE 0.015 0.002 PHE L 71 TRP 0.037 0.003 TRP C 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 ( 3275) covalent geometry : angle 0.62856 / 0.33 ( 4443) SS BOND : bond 0.00230 / 0.12 ( 6) SS BOND : angle 0.61763 / 0.37 ( 12) hydrogen bonds : bond 0.02942 / 1.78 ( 104) hydrogen bonds : angle 6.05999 / 3.92 ( 249) link_BETA1-4 : bond 0.00017 / 0.01 ( 1) link_BETA1-4 : angle 1.03151 / 0.60 ( 3) link_NAG-ASN : bond 0.00156 / 0.08 ( 2) link_NAG-ASN : angle 2.20431 / 1.54 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 71 PHE cc_start: 0.5282 (t80) cc_final: 0.4979 (m-80) REVERT: L 74 THR cc_start: 0.4214 (OUTLIER) cc_final: 0.3843 (p) REVERT: L 103 LYS cc_start: 0.7753 (tptp) cc_final: 0.7392 (tppt) REVERT: C 387 LEU cc_start: 0.8410 (tp) cc_final: 0.8086 (tp) REVERT: C 418 ILE cc_start: 0.9367 (mm) cc_final: 0.9121 (tp) outliers start: 10 outliers final: 8 residues processed: 54 average time/residue: 0.0412 time to fit residues: 2.7854 Evaluate side-chains 52 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 503 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 37 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 23 optimal weight: 0.4980 chunk 2 optimal weight: 0.0070 chunk 27 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.8602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.078346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.071746 restraints weight = 14480.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.073382 restraints weight = 7500.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.074410 restraints weight = 4467.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.075060 restraints weight = 2945.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.075453 restraints weight = 2113.513| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.5850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3284 Z= 0.175 Angle : 0.669 5.917 4464 Z= 0.353 Chirality : 0.045 0.140 487 Planarity : 0.005 0.046 565 Dihedral : 5.154 21.201 447 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 2.91 % Allowed : 15.99 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.93 (0.43), residues: 395 helix: -3.12 (1.14), residues: 15 sheet: 0.12 (0.51), residues: 122 loop : -0.83 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 466 TYR 0.021 0.001 TYR L 92 PHE 0.014 0.002 PHE L 71 TRP 0.053 0.004 TRP C 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.18 ( 3275) covalent geometry : angle 0.66488 / 0.35 ( 4443) SS BOND : bond 0.00252 / 0.13 ( 6) SS BOND : angle 0.59763 / 0.36 ( 12) hydrogen bonds : bond 0.03071 / 1.90 ( 104) hydrogen bonds : angle 6.18606 / 4.01 ( 249) link_BETA1-4 : bond 0.00267 / 0.14 ( 1) link_BETA1-4 : angle 1.13398 / 0.66 ( 3) link_NAG-ASN : bond 0.00194 / 0.10 ( 2) link_NAG-ASN : angle 2.16907 / 1.50 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 74 THR cc_start: 0.4215 (OUTLIER) cc_final: 0.3821 (p) REVERT: C 387 LEU cc_start: 0.8278 (tp) cc_final: 0.8034 (tp) REVERT: C 418 ILE cc_start: 0.9375 (mm) cc_final: 0.9164 (tp) outliers start: 10 outliers final: 9 residues processed: 50 average time/residue: 0.0717 time to fit residues: 4.3789 Evaluate side-chains 47 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 37 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 503 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 10 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 14 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.077619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.071251 restraints weight = 14645.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.072779 restraints weight = 7746.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.073740 restraints weight = 4663.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.074313 restraints weight = 3109.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.074761 restraints weight = 2300.050| |-----------------------------------------------------------------------------| r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.6255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3284 Z= 0.179 Angle : 0.670 6.310 4464 Z= 0.353 Chirality : 0.046 0.148 487 Planarity : 0.005 0.045 565 Dihedral : 5.220 21.454 447 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 3.49 % Allowed : 15.70 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.23 (0.42), residues: 395 helix: -3.40 (0.83), residues: 22 sheet: -0.09 (0.50), residues: 123 loop : -0.95 (0.39), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 509 TYR 0.019 0.002 TYR L 32 PHE 0.011 0.002 PHE C 338 TRP 0.023 0.002 TRP H 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.18 ( 3275) covalent geometry : angle 0.66635 / 0.35 ( 4443) SS BOND : bond 0.00275 / 0.14 ( 6) SS BOND : angle 0.58047 / 0.35 ( 12) hydrogen bonds : bond 0.03033 / 1.88 ( 104) hydrogen bonds : angle 6.23436 / 4.05 ( 249) link_BETA1-4 : bond 0.00136 / 0.07 ( 1) link_BETA1-4 : angle 1.04954 / 0.61 ( 3) link_NAG-ASN : bond 0.00282 / 0.15 ( 2) link_NAG-ASN : angle 2.04949 / 1.50 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 2 ILE cc_start: 0.7825 (mt) cc_final: 0.7578 (mm) REVERT: L 74 THR cc_start: 0.4318 (OUTLIER) cc_final: 0.3962 (p) REVERT: C 387 LEU cc_start: 0.8367 (tp) cc_final: 0.8114 (tp) outliers start: 12 outliers final: 10 residues processed: 49 average time/residue: 0.0593 time to fit residues: 3.7088 Evaluate side-chains 50 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 503 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 14 optimal weight: 1.9990 chunk 22 optimal weight: 0.0570 chunk 19 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 20 optimal weight: 0.4980 chunk 35 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.077715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.071371 restraints weight = 14515.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.072871 restraints weight = 7643.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.073819 restraints weight = 4599.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.074407 restraints weight = 3061.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.074776 restraints weight = 2226.283| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.6473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3284 Z= 0.164 Angle : 0.647 5.813 4464 Z= 0.341 Chirality : 0.047 0.152 487 Planarity : 0.005 0.045 565 Dihedral : 5.213 21.198 447 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 3.20 % Allowed : 16.28 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.37 (0.42), residues: 395 helix: -3.72 (0.63), residues: 34 sheet: 0.21 (0.52), residues: 112 loop : -1.05 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 97 TYR 0.018 0.002 TYR C 423 PHE 0.011 0.001 PHE C 338 TRP 0.039 0.003 TRP C 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 ( 3275) covalent geometry : angle 0.64281 / 0.34 ( 4443) SS BOND : bond 0.00296 / 0.14 ( 6) SS BOND : angle 0.60939 / 0.35 ( 12) hydrogen bonds : bond 0.02958 / 1.86 ( 104) hydrogen bonds : angle 6.14332 / 3.97 ( 249) link_BETA1-4 : bond 0.00113 / 0.06 ( 1) link_BETA1-4 : angle 1.05606 / 0.61 ( 3) link_NAG-ASN : bond 0.00220 / 0.11 ( 2) link_NAG-ASN : angle 2.05221 / 1.44 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 2 ILE cc_start: 0.7845 (mt) cc_final: 0.7586 (mm) REVERT: L 74 THR cc_start: 0.4323 (OUTLIER) cc_final: 0.3995 (p) REVERT: C 387 LEU cc_start: 0.8349 (tp) cc_final: 0.8121 (tp) REVERT: C 468 ILE cc_start: 0.9087 (OUTLIER) cc_final: 0.8612 (tp) outliers start: 11 outliers final: 8 residues processed: 51 average time/residue: 0.0508 time to fit residues: 3.3726 Evaluate side-chains 48 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 503 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 13 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 27 optimal weight: 0.4980 chunk 22 optimal weight: 0.0870 chunk 19 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 29 optimal weight: 0.2980 chunk 35 optimal weight: 0.3980 chunk 20 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.079284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.073069 restraints weight = 14242.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.074539 restraints weight = 7393.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.075472 restraints weight = 4440.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.076076 restraints weight = 2943.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.076488 restraints weight = 2120.176| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.6634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3284 Z= 0.127 Angle : 0.650 7.580 4464 Z= 0.343 Chirality : 0.046 0.145 487 Planarity : 0.004 0.045 565 Dihedral : 5.072 22.726 447 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 3.20 % Allowed : 16.86 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.35 (0.42), residues: 395 helix: -3.70 (0.62), residues: 34 sheet: 0.22 (0.52), residues: 112 loop : -1.02 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 509 TYR 0.012 0.001 TYR C 351 PHE 0.008 0.001 PHE C 338 TRP 0.032 0.003 TRP C 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 ( 3275) covalent geometry : angle 0.64634 / 0.34 ( 4443) SS BOND : bond 0.00260 / 0.12 ( 6) SS BOND : angle 0.50056 / 0.29 ( 12) hydrogen bonds : bond 0.02863 / 1.79 ( 104) hydrogen bonds : angle 5.85746 / 3.76 ( 249) link_BETA1-4 : bond 0.00117 / 0.06 ( 1) link_BETA1-4 : angle 0.97939 / 0.57 ( 3) link_NAG-ASN : bond 0.00215 / 0.11 ( 2) link_NAG-ASN : angle 1.92111 / 1.38 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 74 THR cc_start: 0.4060 (OUTLIER) cc_final: 0.3736 (p) REVERT: C 468 ILE cc_start: 0.9172 (OUTLIER) cc_final: 0.8651 (tp) outliers start: 11 outliers final: 9 residues processed: 50 average time/residue: 0.0815 time to fit residues: 4.9678 Evaluate side-chains 47 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 503 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 22 optimal weight: 0.0270 chunk 13 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 25 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.078558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.072162 restraints weight = 14511.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.073653 restraints weight = 7533.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.074573 restraints weight = 4527.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.075166 restraints weight = 3038.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.075583 restraints weight = 2228.198| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.6706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3284 Z= 0.144 Angle : 0.626 5.980 4464 Z= 0.330 Chirality : 0.046 0.156 487 Planarity : 0.005 0.045 565 Dihedral : 5.058 23.882 447 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 3.20 % Allowed : 17.73 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.33 (0.42), residues: 395 helix: -3.68 (0.62), residues: 34 sheet: 0.28 (0.51), residues: 112 loop : -1.05 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 509 TYR 0.010 0.001 TYR C 365 PHE 0.010 0.001 PHE C 338 TRP 0.034 0.003 TRP C 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 3275) covalent geometry : angle 0.62198 / 0.33 ( 4443) SS BOND : bond 0.00339 / 0.16 ( 6) SS BOND : angle 0.68207 / 0.44 ( 12) hydrogen bonds : bond 0.03007 / 1.86 ( 104) hydrogen bonds : angle 5.86973 / 3.79 ( 249) link_BETA1-4 : bond 0.00082 / 0.04 ( 1) link_BETA1-4 : angle 1.00288 / 0.59 ( 3) link_NAG-ASN : bond 0.00188 / 0.10 ( 2) link_NAG-ASN : angle 2.02108 / 1.45 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 810.85 seconds wall clock time: 14 minutes 43.66 seconds (883.66 seconds total)