Starting phenix.real_space_refine on Wed Jun 4 15:36:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wb5_32395/06_2025/7wb5_32395.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wb5_32395/06_2025/7wb5_32395.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wb5_32395/06_2025/7wb5_32395.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wb5_32395/06_2025/7wb5_32395.map" model { file = "/net/cci-nas-00/data/ceres_data/7wb5_32395/06_2025/7wb5_32395.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wb5_32395/06_2025/7wb5_32395.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.022 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 15 5.16 5 C 2077 2.51 5 N 533 2.21 5 O 631 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 3256 Number of models: 1 Model: "" Number of chains: 4 Chain: "H" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 928 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "L" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} 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: "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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.47, per 1000 atoms: 1.07 Number of scatterers: 3256 At special positions: 0 Unit cell: (72.36, 88.56, 72.36, 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 631 8.00 N 533 7.00 C 2077 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS R 480 " - pdb=" SG CYS R 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 A 2 " - " BMA A 3 " NAG-ASN " NAG A 1 " - " ASN R 343 " Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 403.2 milliseconds 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 746 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 12 sheets defined 4.4% alpha, 25.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'R' and resid 349 through 353 Processing helix chain 'R' and resid 364 through 370 removed outlier: 4.598A pdb=" N LEU R 368 " --> pdb=" O ASP R 364 " (cutoff:3.500A) Processing helix chain 'R' and resid 416 through 421 Processing sheet with id=AA1, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.682A pdb=" N LYS H 12 " --> pdb=" O THR H 116 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'H' and resid 46 through 47 removed outlier: 3.906A pdb=" N THR H 113 " --> pdb=" O TYR H 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 49 through 51 removed outlier: 3.533A pdb=" N TRP H 50 " --> pdb=" O THR H 59 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 68 through 70 Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.846A pdb=" N ILE L 21 " --> pdb=" O LEU L 73 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU L 73 " --> pdb=" O ILE L 21 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N SER L 63 " --> pdb=" O THR L 74 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.595A pdb=" N LEU L 11 " --> pdb=" O LYS L 103 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLU L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 53 through 54 removed outlier: 3.572A pdb=" N GLN L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 354 through 358 removed outlier: 3.884A pdb=" N ILE R 434 " --> pdb=" O VAL R 511 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N CYS R 432 " --> pdb=" O LEU R 513 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'R' and resid 354 through 358 Processing sheet with id=AB2, first strand: chain 'R' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'R' and resid 473 through 474 73 hydrogen bonds defined for protein. 171 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: 0.77 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 734 1.33 - 1.45: 857 1.45 - 1.57: 1735 1.57 - 1.69: 1 1.69 - 1.82: 18 Bond restraints: 3345 Sorted by residual: bond pdb=" CA SER R 438 " pdb=" CB SER R 438 " ideal model delta sigma weight residual 1.528 1.475 0.053 1.35e-02 5.49e+03 1.53e+01 bond pdb=" CA SER R 349 " pdb=" CB SER R 349 " ideal model delta sigma weight residual 1.529 1.467 0.062 1.64e-02 3.72e+03 1.43e+01 bond pdb=" N LEU R 452 " pdb=" CA LEU R 452 " ideal model delta sigma weight residual 1.452 1.495 -0.043 1.22e-02 6.72e+03 1.23e+01 bond pdb=" N VAL R 433 " pdb=" CA VAL R 433 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.25e-02 6.40e+03 1.07e+01 bond pdb=" N LYS R 378 " pdb=" CA LYS R 378 " ideal model delta sigma weight residual 1.457 1.499 -0.041 1.29e-02 6.01e+03 1.03e+01 ... (remaining 3340 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 4160 2.59 - 5.17: 364 5.17 - 7.76: 19 7.76 - 10.34: 3 10.34 - 12.93: 2 Bond angle restraints: 4548 Sorted by residual: angle pdb=" CA PRO L 80 " pdb=" N PRO L 80 " pdb=" CD PRO L 80 " ideal model delta sigma weight residual 112.00 99.07 12.93 1.40e+00 5.10e-01 8.52e+01 angle pdb=" CA TRP R 436 " pdb=" CB TRP R 436 " pdb=" CG TRP R 436 " ideal model delta sigma weight residual 113.60 123.83 -10.23 1.90e+00 2.77e-01 2.90e+01 angle pdb=" CA PHE R 400 " pdb=" CB PHE R 400 " pdb=" CG PHE R 400 " ideal model delta sigma weight residual 113.80 118.30 -4.50 1.00e+00 1.00e+00 2.03e+01 angle pdb=" N PRO L 80 " pdb=" CD PRO L 80 " pdb=" CG PRO L 80 " ideal model delta sigma weight residual 103.20 96.90 6.30 1.50e+00 4.44e-01 1.77e+01 angle pdb=" N LEU R 387 " pdb=" CA LEU R 387 " pdb=" C LEU R 387 " ideal model delta sigma weight residual 114.75 109.56 5.19 1.26e+00 6.30e-01 1.69e+01 ... (remaining 4543 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.52: 1718 21.52 - 43.04: 173 43.04 - 64.55: 66 64.55 - 86.07: 12 86.07 - 107.59: 12 Dihedral angle restraints: 1981 sinusoidal: 801 harmonic: 1180 Sorted by residual: dihedral pdb=" CA VAL L 29 " pdb=" C VAL L 29 " pdb=" N SER L 30 " pdb=" CA SER L 30 " ideal model delta harmonic sigma weight residual 180.00 -139.90 -40.10 0 5.00e+00 4.00e-02 6.43e+01 dihedral pdb=" CA PHE H 106 " pdb=" C PHE H 106 " pdb=" N ASP H 107 " pdb=" CA ASP H 107 " ideal model delta harmonic sigma weight residual 180.00 -146.68 -33.32 0 5.00e+00 4.00e-02 4.44e+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 93.00 136.78 -43.78 1 1.00e+01 1.00e-02 2.67e+01 ... (remaining 1978 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 417 0.119 - 0.238: 63 0.238 - 0.356: 5 0.356 - 0.475: 0 0.475 - 0.593: 2 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 -2.23 -0.17 2.00e-02 2.50e+03 6.89e+01 chirality pdb=" C1 BMA A 3 " pdb=" O4 NAG A 2 " pdb=" C2 BMA A 3 " pdb=" O5 BMA A 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.29e+01 chirality pdb=" C1 NAG A 1 " pdb=" ND2 ASN R 343 " pdb=" C2 NAG A 1 " pdb=" O5 NAG A 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.81 -0.59 2.00e-01 2.50e+01 8.81e+00 ... (remaining 484 not shown) Planarity restraints: 582 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 2 " 0.304 2.00e-02 2.50e+03 2.62e-01 8.61e+02 pdb=" C7 NAG A 2 " -0.065 2.00e-02 2.50e+03 pdb=" C8 NAG A 2 " 0.009 2.00e-02 2.50e+03 pdb=" N2 NAG A 2 " -0.453 2.00e-02 2.50e+03 pdb=" O7 NAG A 2 " 0.205 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 1 " -0.292 2.00e-02 2.50e+03 2.51e-01 7.91e+02 pdb=" C7 NAG A 1 " 0.068 2.00e-02 2.50e+03 pdb=" C8 NAG A 1 " -0.164 2.00e-02 2.50e+03 pdb=" N2 NAG A 1 " 0.443 2.00e-02 2.50e+03 pdb=" O7 NAG A 1 " -0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN L 79 " -0.111 5.00e-02 4.00e+02 1.57e-01 3.92e+01 pdb=" N PRO L 80 " 0.270 5.00e-02 4.00e+02 pdb=" CA PRO L 80 " -0.083 5.00e-02 4.00e+02 pdb=" CD PRO L 80 " -0.076 5.00e-02 4.00e+02 ... (remaining 579 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 281 2.73 - 3.27: 3255 3.27 - 3.82: 5356 3.82 - 4.36: 6706 4.36 - 4.90: 11080 Nonbonded interactions: 26678 Sorted by model distance: nonbonded pdb=" O ILE L 21 " pdb=" OG1 THR L 72 " model vdw 2.188 3.040 nonbonded pdb=" OG SER H 7 " pdb=" OG SER H 21 " model vdw 2.216 3.040 nonbonded pdb=" OE1 GLN H 6 " pdb=" OG1 THR H 113 " model vdw 2.319 3.040 nonbonded pdb=" OG SER L 26 " pdb=" OE1 GLN L 27 " model vdw 2.405 3.040 nonbonded pdb=" O VAL H 76 " pdb=" OG SER H 77 " model vdw 2.421 3.040 ... (remaining 26673 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: 3.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.810 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 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 : 0.011 0.132 3353 Z= 0.659 Angle : 1.420 12.925 4567 Z= 0.928 Chirality : 0.090 0.593 487 Planarity : 0.018 0.262 581 Dihedral : 21.949 107.591 1220 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 18.30 Ramachandran Plot: Outliers : 2.24 % Allowed : 18.16 % Favored : 79.60 % Rotamer: Outliers : 14.00 % Allowed : 7.43 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.52 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.90 (0.36), residues: 402 helix: -4.22 (0.64), residues: 21 sheet: -3.58 (0.39), residues: 121 loop : -3.14 (0.35), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.092 0.006 TRP H 109 HIS 0.001 0.001 HIS L 34 PHE 0.023 0.003 PHE R 400 TYR 0.024 0.003 TYR L 49 ARG 0.007 0.001 ARG L 61 Details of bonding type rmsd link_NAG-ASN : bond 0.02467 ( 1) link_NAG-ASN : angle 2.58754 ( 3) link_BETA1-4 : bond 0.00673 ( 2) link_BETA1-4 : angle 4.14677 ( 6) hydrogen bonds : bond 0.24913 ( 63) hydrogen bonds : angle 11.58444 ( 171) SS BOND : bond 0.00729 ( 5) SS BOND : angle 2.86471 ( 10) covalent geometry : bond 0.01062 ( 3345) covalent geometry : angle 1.40708 ( 4548) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 125 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: H 83 ILE cc_start: 0.9173 (tt) cc_final: 0.8932 (tt) REVERT: L 74 THR cc_start: 0.7091 (m) cc_final: 0.6553 (m) REVERT: L 79 GLN cc_start: 0.8296 (mp10) cc_final: 0.7818 (mp10) REVERT: R 369 TYR cc_start: 0.7978 (t80) cc_final: 0.7755 (t80) REVERT: R 387 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8498 (tt) REVERT: R 454 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7654 (mtp-110) REVERT: R 493 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.7989 (tm-30) outliers start: 49 outliers final: 12 residues processed: 150 average time/residue: 0.1905 time to fit residues: 33.4395 Evaluate side-chains 122 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 387 LEU Chi-restraints excluded: chain R residue 407 VAL Chi-restraints excluded: chain R residue 410 ILE Chi-restraints excluded: chain R residue 422 ASN Chi-restraints excluded: chain R residue 425 LEU Chi-restraints excluded: chain R residue 430 THR Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain R residue 436 TRP Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain R residue 443 SER Chi-restraints excluded: chain R residue 454 ARG Chi-restraints excluded: chain R residue 466 ARG Chi-restraints excluded: chain R residue 472 ILE Chi-restraints excluded: chain R residue 493 GLN Chi-restraints excluded: chain R residue 516 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 30 optimal weight: 0.4980 chunk 11 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 0.1980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 35 ASN H 82 GLN ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 481 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.139944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.117011 restraints weight = 5133.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.119602 restraints weight = 3330.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.121330 restraints weight = 2493.985| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3353 Z= 0.181 Angle : 0.834 7.995 4567 Z= 0.422 Chirality : 0.050 0.200 487 Planarity : 0.007 0.085 581 Dihedral : 17.717 93.006 544 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.50 % Allowed : 11.44 % Favored : 88.06 % Rotamer: Outliers : 7.14 % Allowed : 19.14 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.48 (0.36), residues: 402 helix: -3.40 (0.78), residues: 21 sheet: -3.11 (0.42), residues: 114 loop : -3.03 (0.34), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP H 109 HIS 0.002 0.001 HIS L 34 PHE 0.027 0.002 PHE R 515 TYR 0.018 0.002 TYR L 49 ARG 0.006 0.001 ARG L 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00331 ( 1) link_NAG-ASN : angle 1.66321 ( 3) link_BETA1-4 : bond 0.00957 ( 2) link_BETA1-4 : angle 3.73156 ( 6) hydrogen bonds : bond 0.04465 ( 63) hydrogen bonds : angle 7.22489 ( 171) SS BOND : bond 0.00264 ( 5) SS BOND : angle 1.37732 ( 10) covalent geometry : bond 0.00412 ( 3345) covalent geometry : angle 0.82103 ( 4548) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 60 TYR cc_start: 0.8391 (m-80) cc_final: 0.8030 (m-10) REVERT: L 79 GLN cc_start: 0.8421 (mp10) cc_final: 0.7707 (mp10) REVERT: R 387 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8400 (tt) REVERT: R 454 ARG cc_start: 0.8019 (mtp180) cc_final: 0.6649 (mtp85) REVERT: R 462 LYS cc_start: 0.8526 (pptt) cc_final: 0.8094 (ptmm) REVERT: R 467 ASP cc_start: 0.6022 (p0) cc_final: 0.5224 (p0) REVERT: R 493 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.7727 (tm-30) REVERT: R 516 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7491 (pp20) outliers start: 25 outliers final: 18 residues processed: 123 average time/residue: 0.1858 time to fit residues: 26.8459 Evaluate side-chains 118 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 82 GLN Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain R residue 387 LEU Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 407 VAL Chi-restraints excluded: chain R residue 425 LEU Chi-restraints excluded: chain R residue 430 THR Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain R residue 436 TRP Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain R residue 443 SER Chi-restraints excluded: chain R residue 452 LEU Chi-restraints excluded: chain R residue 466 ARG Chi-restraints excluded: chain R residue 472 ILE Chi-restraints excluded: chain R residue 478 THR Chi-restraints excluded: chain R residue 493 GLN Chi-restraints excluded: chain R residue 495 TYR Chi-restraints excluded: chain R residue 516 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 5 optimal weight: 0.5980 chunk 21 optimal weight: 0.2980 chunk 25 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 82 GLN ** L 89 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 = 0.3797 r_free = 0.3797 target = 0.141340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.117107 restraints weight = 4980.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.119938 restraints weight = 3145.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.121833 restraints weight = 2319.948| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3353 Z= 0.158 Angle : 0.763 9.531 4567 Z= 0.376 Chirality : 0.049 0.229 487 Planarity : 0.006 0.078 581 Dihedral : 14.484 79.267 536 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.50 % Allowed : 9.95 % Favored : 89.55 % Rotamer: Outliers : 7.14 % Allowed : 18.29 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.05 (0.37), residues: 402 helix: -3.72 (0.71), residues: 21 sheet: -2.44 (0.46), residues: 114 loop : -2.88 (0.34), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP H 109 HIS 0.001 0.001 HIS L 34 PHE 0.025 0.002 PHE R 515 TYR 0.022 0.002 TYR H 105 ARG 0.003 0.000 ARG R 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00375 ( 1) link_NAG-ASN : angle 1.20289 ( 3) link_BETA1-4 : bond 0.00812 ( 2) link_BETA1-4 : angle 3.99149 ( 6) hydrogen bonds : bond 0.03704 ( 63) hydrogen bonds : angle 6.58151 ( 171) SS BOND : bond 0.00364 ( 5) SS BOND : angle 1.17436 ( 10) covalent geometry : bond 0.00367 ( 3345) covalent geometry : angle 0.74832 ( 4548) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 60 TYR cc_start: 0.8344 (m-80) cc_final: 0.8069 (m-10) REVERT: L 79 GLN cc_start: 0.8465 (mp10) cc_final: 0.8026 (mp10) REVERT: L 100 GLN cc_start: 0.7370 (tm-30) cc_final: 0.7136 (tm-30) REVERT: R 386 LYS cc_start: 0.4625 (pttt) cc_final: 0.3245 (pttt) REVERT: R 387 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8267 (tt) REVERT: R 493 GLN cc_start: 0.8075 (tm-30) cc_final: 0.7468 (tm-30) outliers start: 25 outliers final: 20 residues processed: 126 average time/residue: 0.1804 time to fit residues: 26.7385 Evaluate side-chains 121 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 83 ILE Chi-restraints excluded: chain H residue 107 ASP Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain R residue 345 THR Chi-restraints excluded: chain R residue 387 LEU Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 407 VAL Chi-restraints excluded: chain R residue 430 THR Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain R residue 443 SER Chi-restraints excluded: chain R residue 452 LEU Chi-restraints excluded: chain R residue 466 ARG Chi-restraints excluded: chain R residue 472 ILE Chi-restraints excluded: chain R residue 478 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 8 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 0.0980 chunk 6 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 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 = 0.3807 r_free = 0.3807 target = 0.141612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.117441 restraints weight = 5043.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.120335 restraints weight = 3084.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.122280 restraints weight = 2238.809| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3353 Z= 0.165 Angle : 0.762 9.669 4567 Z= 0.375 Chirality : 0.048 0.246 487 Planarity : 0.006 0.082 581 Dihedral : 12.016 64.430 526 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.50 % Allowed : 8.46 % Favored : 91.04 % Rotamer: Outliers : 8.29 % Allowed : 21.71 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.12 (0.37), residues: 402 helix: -3.59 (0.82), residues: 19 sheet: -2.54 (0.44), residues: 125 loop : -2.90 (0.34), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.004 TRP H 109 HIS 0.002 0.001 HIS L 34 PHE 0.020 0.002 PHE R 392 TYR 0.020 0.002 TYR H 105 ARG 0.007 0.001 ARG L 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00334 ( 1) link_NAG-ASN : angle 1.04261 ( 3) link_BETA1-4 : bond 0.00886 ( 2) link_BETA1-4 : angle 3.98691 ( 6) hydrogen bonds : bond 0.03506 ( 63) hydrogen bonds : angle 6.07344 ( 171) SS BOND : bond 0.00517 ( 5) SS BOND : angle 1.09437 ( 10) covalent geometry : bond 0.00378 ( 3345) covalent geometry : angle 0.74723 ( 4548) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 96 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: H 34 MET cc_start: 0.8900 (tpp) cc_final: 0.8659 (tpp) REVERT: H 60 TYR cc_start: 0.8396 (m-80) cc_final: 0.8087 (m-10) REVERT: L 62 PHE cc_start: 0.7897 (OUTLIER) cc_final: 0.7023 (p90) REVERT: L 79 GLN cc_start: 0.8440 (mp10) cc_final: 0.7948 (mp10) REVERT: L 100 GLN cc_start: 0.7381 (tm-30) cc_final: 0.7130 (tm-30) REVERT: R 386 LYS cc_start: 0.4271 (pttt) cc_final: 0.3068 (pttt) REVERT: R 387 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8164 (tt) REVERT: R 466 ARG cc_start: 0.7361 (OUTLIER) cc_final: 0.6281 (ptp-110) REVERT: R 493 GLN cc_start: 0.8175 (tm-30) cc_final: 0.7479 (tm-30) outliers start: 29 outliers final: 19 residues processed: 115 average time/residue: 0.1699 time to fit residues: 23.1692 Evaluate side-chains 108 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 83 ILE Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain R residue 345 THR Chi-restraints excluded: chain R residue 387 LEU Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain R residue 443 SER Chi-restraints excluded: chain R residue 452 LEU Chi-restraints excluded: chain R residue 466 ARG Chi-restraints excluded: chain R residue 472 ILE Chi-restraints excluded: chain R residue 478 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 8 optimal weight: 0.0980 chunk 25 optimal weight: 0.9990 chunk 34 optimal weight: 0.3980 chunk 2 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 422 ASN ** 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 = 0.3815 r_free = 0.3815 target = 0.142555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.118518 restraints weight = 5075.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.122162 restraints weight = 4030.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.123100 restraints weight = 2548.579| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3353 Z= 0.148 Angle : 0.733 8.751 4567 Z= 0.360 Chirality : 0.047 0.197 487 Planarity : 0.006 0.081 581 Dihedral : 10.033 50.747 524 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.70 % Favored : 90.05 % Rotamer: Outliers : 8.29 % Allowed : 22.00 % Favored : 69.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.04 (0.37), residues: 402 helix: -3.62 (0.78), residues: 19 sheet: -2.48 (0.45), residues: 121 loop : -2.85 (0.34), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP H 109 HIS 0.001 0.001 HIS L 34 PHE 0.014 0.001 PHE R 392 TYR 0.021 0.002 TYR H 105 ARG 0.004 0.001 ARG R 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00151 ( 1) link_NAG-ASN : angle 0.62688 ( 3) link_BETA1-4 : bond 0.00899 ( 2) link_BETA1-4 : angle 3.88873 ( 6) hydrogen bonds : bond 0.03268 ( 63) hydrogen bonds : angle 5.99770 ( 171) SS BOND : bond 0.00144 ( 5) SS BOND : angle 1.20505 ( 10) covalent geometry : bond 0.00339 ( 3345) covalent geometry : angle 0.71850 ( 4548) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 97 time to evaluate : 0.380 Fit side-chains REVERT: H 43 GLN cc_start: 0.7074 (mp10) cc_final: 0.6581 (mp10) REVERT: H 60 TYR cc_start: 0.8394 (m-80) cc_final: 0.8080 (m-10) REVERT: L 62 PHE cc_start: 0.7913 (OUTLIER) cc_final: 0.7045 (p90) REVERT: L 79 GLN cc_start: 0.8474 (mp10) cc_final: 0.8032 (mp10) REVERT: L 100 GLN cc_start: 0.7460 (tm-30) cc_final: 0.7200 (tm-30) REVERT: R 386 LYS cc_start: 0.4242 (pttt) cc_final: 0.3077 (pttt) REVERT: R 387 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8189 (tt) REVERT: R 408 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.8428 (ptm-80) REVERT: R 409 GLN cc_start: 0.8298 (mt0) cc_final: 0.7651 (mt0) REVERT: R 466 ARG cc_start: 0.7288 (OUTLIER) cc_final: 0.6216 (ptp-110) REVERT: R 493 GLN cc_start: 0.8117 (tm-30) cc_final: 0.7516 (tm-30) outliers start: 29 outliers final: 21 residues processed: 112 average time/residue: 0.1697 time to fit residues: 22.7423 Evaluate side-chains 117 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 92 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 83 ILE Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain R residue 345 THR Chi-restraints excluded: chain R residue 387 LEU Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 407 VAL Chi-restraints excluded: chain R residue 408 ARG Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain R residue 452 LEU Chi-restraints excluded: chain R residue 466 ARG Chi-restraints excluded: chain R residue 472 ILE Chi-restraints excluded: chain R residue 478 THR Chi-restraints excluded: chain R residue 495 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 22 optimal weight: 0.9990 chunk 25 optimal weight: 0.0270 chunk 6 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 10 optimal weight: 0.3980 chunk 17 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 38 optimal weight: 0.0770 chunk 26 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 422 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.143943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.120709 restraints weight = 5171.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.121964 restraints weight = 3417.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.123892 restraints weight = 3188.209| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3353 Z= 0.137 Angle : 0.723 8.184 4567 Z= 0.358 Chirality : 0.047 0.184 487 Planarity : 0.006 0.078 581 Dihedral : 9.347 52.027 523 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.21 % Favored : 91.54 % Rotamer: Outliers : 8.29 % Allowed : 21.71 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.96 (0.37), residues: 402 helix: -3.35 (0.87), residues: 19 sheet: -2.41 (0.45), residues: 115 loop : -2.83 (0.33), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP H 109 HIS 0.002 0.001 HIS L 34 PHE 0.012 0.001 PHE R 392 TYR 0.023 0.002 TYR H 105 ARG 0.006 0.001 ARG R 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00074 ( 1) link_NAG-ASN : angle 0.60659 ( 3) link_BETA1-4 : bond 0.01231 ( 2) link_BETA1-4 : angle 3.93329 ( 6) hydrogen bonds : bond 0.03177 ( 63) hydrogen bonds : angle 5.72924 ( 171) SS BOND : bond 0.00202 ( 5) SS BOND : angle 1.12298 ( 10) covalent geometry : bond 0.00320 ( 3345) covalent geometry : angle 0.70771 ( 4548) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 0.390 Fit side-chains revert: symmetry clash REVERT: H 60 TYR cc_start: 0.8293 (m-80) cc_final: 0.7931 (m-10) REVERT: H 95 TYR cc_start: 0.7934 (m-10) cc_final: 0.7732 (m-80) REVERT: H 109 TRP cc_start: 0.7386 (OUTLIER) cc_final: 0.6988 (p90) REVERT: L 62 PHE cc_start: 0.7909 (OUTLIER) cc_final: 0.7047 (p90) REVERT: L 79 GLN cc_start: 0.8513 (mp10) cc_final: 0.8011 (mp10) REVERT: L 100 GLN cc_start: 0.7386 (tm-30) cc_final: 0.7183 (tm-30) REVERT: R 386 LYS cc_start: 0.4211 (pttt) cc_final: 0.2982 (pttt) REVERT: R 387 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8145 (tt) REVERT: R 408 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.8147 (ptm160) REVERT: R 454 ARG cc_start: 0.7957 (mtp180) cc_final: 0.7435 (mtp85) REVERT: R 467 ASP cc_start: 0.6588 (p0) cc_final: 0.5896 (p0) REVERT: R 493 GLN cc_start: 0.8117 (tm-30) cc_final: 0.7547 (tm-30) outliers start: 29 outliers final: 21 residues processed: 117 average time/residue: 0.1791 time to fit residues: 24.6291 Evaluate side-chains 121 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 82 GLN Chi-restraints excluded: chain H residue 83 ILE Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 109 TRP Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain R residue 345 THR Chi-restraints excluded: chain R residue 387 LEU Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 407 VAL Chi-restraints excluded: chain R residue 408 ARG Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain R residue 466 ARG Chi-restraints excluded: chain R residue 472 ILE Chi-restraints excluded: chain R residue 478 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 38 optimal weight: 0.5980 chunk 4 optimal weight: 0.3980 chunk 21 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 15 optimal weight: 0.0270 chunk 35 optimal weight: 3.9990 chunk 16 optimal weight: 0.4980 chunk 36 optimal weight: 3.9990 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 82 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 409 GLN R 414 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.143974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.119678 restraints weight = 5048.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.123287 restraints weight = 4048.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.124187 restraints weight = 2468.901| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3353 Z= 0.137 Angle : 0.717 7.291 4567 Z= 0.357 Chirality : 0.046 0.159 487 Planarity : 0.006 0.077 581 Dihedral : 8.831 53.337 523 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.46 % Favored : 91.29 % Rotamer: Outliers : 7.71 % Allowed : 21.71 % Favored : 70.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.82 (0.37), residues: 402 helix: -3.21 (1.00), residues: 19 sheet: -2.43 (0.46), residues: 110 loop : -2.68 (0.33), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP H 109 HIS 0.000 0.000 HIS L 34 PHE 0.012 0.001 PHE R 392 TYR 0.023 0.002 TYR H 105 ARG 0.003 0.001 ARG R 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00094 ( 1) link_NAG-ASN : angle 0.62285 ( 3) link_BETA1-4 : bond 0.01089 ( 2) link_BETA1-4 : angle 4.00718 ( 6) hydrogen bonds : bond 0.02983 ( 63) hydrogen bonds : angle 5.65514 ( 171) SS BOND : bond 0.00118 ( 5) SS BOND : angle 1.10100 ( 10) covalent geometry : bond 0.00321 ( 3345) covalent geometry : angle 0.70199 ( 4548) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 97 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: H 25 SER cc_start: 0.7662 (t) cc_final: 0.7260 (m) REVERT: H 60 TYR cc_start: 0.8309 (m-80) cc_final: 0.7971 (m-10) REVERT: H 95 TYR cc_start: 0.7891 (m-10) cc_final: 0.7681 (m-80) REVERT: H 109 TRP cc_start: 0.7517 (OUTLIER) cc_final: 0.7168 (p90) REVERT: L 62 PHE cc_start: 0.7907 (OUTLIER) cc_final: 0.6972 (p90) REVERT: L 79 GLN cc_start: 0.8524 (mp10) cc_final: 0.7950 (mp10) REVERT: R 386 LYS cc_start: 0.4174 (pttt) cc_final: 0.2937 (pttt) REVERT: R 387 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8070 (tt) REVERT: R 408 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.8356 (ptm160) REVERT: R 454 ARG cc_start: 0.7765 (mtp180) cc_final: 0.7543 (mtp85) REVERT: R 493 GLN cc_start: 0.8105 (tm-30) cc_final: 0.7533 (tm-30) outliers start: 27 outliers final: 18 residues processed: 111 average time/residue: 0.1796 time to fit residues: 23.4759 Evaluate side-chains 116 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 83 ILE Chi-restraints excluded: chain H residue 109 TRP Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain R residue 345 THR Chi-restraints excluded: chain R residue 387 LEU Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 407 VAL Chi-restraints excluded: chain R residue 408 ARG Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain R residue 452 LEU Chi-restraints excluded: chain R residue 466 ARG Chi-restraints excluded: chain R residue 472 ILE Chi-restraints excluded: chain R residue 478 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 34 optimal weight: 0.2980 chunk 32 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 25 optimal weight: 0.0470 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 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 = 0.3892 r_free = 0.3892 target = 0.148884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.124298 restraints weight = 4914.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.127157 restraints weight = 3252.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.129037 restraints weight = 2476.118| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3353 Z= 0.152 Angle : 0.746 7.298 4567 Z= 0.375 Chirality : 0.047 0.199 487 Planarity : 0.006 0.077 581 Dihedral : 8.315 55.840 521 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.21 % Favored : 91.54 % Rotamer: Outliers : 6.57 % Allowed : 24.00 % Favored : 69.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.64 (0.37), residues: 402 helix: -3.10 (1.01), residues: 19 sheet: -2.31 (0.46), residues: 110 loop : -2.55 (0.33), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP H 109 HIS 0.001 0.000 HIS L 34 PHE 0.011 0.001 PHE R 392 TYR 0.023 0.002 TYR H 105 ARG 0.005 0.001 ARG L 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00131 ( 1) link_NAG-ASN : angle 0.55138 ( 3) link_BETA1-4 : bond 0.01148 ( 2) link_BETA1-4 : angle 4.10955 ( 6) hydrogen bonds : bond 0.03018 ( 63) hydrogen bonds : angle 5.62146 ( 171) SS BOND : bond 0.00181 ( 5) SS BOND : angle 1.06745 ( 10) covalent geometry : bond 0.00351 ( 3345) covalent geometry : angle 0.73015 ( 4548) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: H 25 SER cc_start: 0.7657 (t) cc_final: 0.7245 (m) REVERT: H 60 TYR cc_start: 0.8345 (m-80) cc_final: 0.7888 (m-10) REVERT: H 109 TRP cc_start: 0.6990 (OUTLIER) cc_final: 0.6729 (p90) REVERT: L 62 PHE cc_start: 0.7961 (OUTLIER) cc_final: 0.6995 (p90) REVERT: L 79 GLN cc_start: 0.8521 (mp10) cc_final: 0.7958 (mp10) REVERT: R 386 LYS cc_start: 0.4200 (pttt) cc_final: 0.3033 (pttt) REVERT: R 387 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8090 (tt) REVERT: R 408 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.8362 (ptm160) REVERT: R 454 ARG cc_start: 0.7796 (mtp180) cc_final: 0.7568 (mtp85) REVERT: R 493 GLN cc_start: 0.8117 (tm-30) cc_final: 0.7656 (tm-30) outliers start: 23 outliers final: 17 residues processed: 109 average time/residue: 0.1783 time to fit residues: 22.8468 Evaluate side-chains 115 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 83 ILE Chi-restraints excluded: chain H residue 109 TRP Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain R residue 345 THR Chi-restraints excluded: chain R residue 387 LEU Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 407 VAL Chi-restraints excluded: chain R residue 408 ARG Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain R residue 466 ARG Chi-restraints excluded: chain R residue 472 ILE Chi-restraints excluded: chain R residue 478 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 16 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 19 optimal weight: 0.2980 chunk 35 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 25 optimal weight: 0.2980 chunk 5 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 15 optimal weight: 0.2980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 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 = 0.3958 r_free = 0.3958 target = 0.152111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.128421 restraints weight = 4924.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.131086 restraints weight = 3344.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.132731 restraints weight = 2585.401| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3353 Z= 0.150 Angle : 0.761 7.895 4567 Z= 0.383 Chirality : 0.048 0.217 487 Planarity : 0.006 0.077 581 Dihedral : 8.134 59.931 521 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.71 % Favored : 91.04 % Rotamer: Outliers : 5.43 % Allowed : 26.00 % Favored : 68.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.49 (0.38), residues: 402 helix: -3.29 (0.92), residues: 19 sheet: -2.22 (0.44), residues: 115 loop : -2.39 (0.35), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.003 TRP H 109 HIS 0.000 0.000 HIS L 34 PHE 0.020 0.002 PHE H 106 TYR 0.025 0.002 TYR H 105 ARG 0.006 0.001 ARG L 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00043 ( 1) link_NAG-ASN : angle 0.57756 ( 3) link_BETA1-4 : bond 0.01180 ( 2) link_BETA1-4 : angle 4.18143 ( 6) hydrogen bonds : bond 0.03032 ( 63) hydrogen bonds : angle 5.72450 ( 171) SS BOND : bond 0.00166 ( 5) SS BOND : angle 1.03230 ( 10) covalent geometry : bond 0.00346 ( 3345) covalent geometry : angle 0.74554 ( 4548) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.388 Fit side-chains revert: symmetry clash REVERT: H 2 VAL cc_start: 0.7585 (m) cc_final: 0.7309 (m) REVERT: H 25 SER cc_start: 0.7577 (t) cc_final: 0.7207 (m) REVERT: H 60 TYR cc_start: 0.8251 (m-80) cc_final: 0.7893 (m-10) REVERT: L 62 PHE cc_start: 0.7989 (OUTLIER) cc_final: 0.6983 (p90) REVERT: L 79 GLN cc_start: 0.8529 (mp10) cc_final: 0.8093 (mp10) REVERT: R 386 LYS cc_start: 0.4376 (pttt) cc_final: 0.3051 (pttt) REVERT: R 387 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8048 (tt) REVERT: R 453 TYR cc_start: 0.8648 (p90) cc_final: 0.8430 (p90) REVERT: R 493 GLN cc_start: 0.7962 (tm-30) cc_final: 0.7458 (tm-30) outliers start: 19 outliers final: 11 residues processed: 107 average time/residue: 0.1857 time to fit residues: 23.7565 Evaluate side-chains 107 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 83 ILE Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain R residue 345 THR Chi-restraints excluded: chain R residue 387 LEU Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 472 ILE Chi-restraints excluded: chain R residue 478 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 17 optimal weight: 3.9990 chunk 5 optimal weight: 0.2980 chunk 15 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 12 optimal weight: 0.3980 chunk 35 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 22 optimal weight: 0.0370 chunk 18 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 414 GLN R 474 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.153953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.130344 restraints weight = 4851.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.133058 restraints weight = 3347.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.134653 restraints weight = 2590.403| |-----------------------------------------------------------------------------| r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.4339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3353 Z= 0.151 Angle : 0.786 7.952 4567 Z= 0.395 Chirality : 0.049 0.189 487 Planarity : 0.007 0.077 581 Dihedral : 7.521 51.246 515 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.96 % Favored : 91.04 % Rotamer: Outliers : 4.57 % Allowed : 26.86 % Favored : 68.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.40 (0.38), residues: 402 helix: -3.62 (0.89), residues: 19 sheet: -2.10 (0.46), residues: 112 loop : -2.34 (0.35), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.004 TRP H 109 HIS 0.001 0.001 HIS L 34 PHE 0.020 0.001 PHE L 83 TYR 0.026 0.002 TYR H 105 ARG 0.011 0.001 ARG H 65 Details of bonding type rmsd link_NAG-ASN : bond 0.00095 ( 1) link_NAG-ASN : angle 0.62417 ( 3) link_BETA1-4 : bond 0.01242 ( 2) link_BETA1-4 : angle 4.35027 ( 6) hydrogen bonds : bond 0.02929 ( 63) hydrogen bonds : angle 5.74950 ( 171) SS BOND : bond 0.00300 ( 5) SS BOND : angle 1.20853 ( 10) covalent geometry : bond 0.00351 ( 3345) covalent geometry : angle 0.76892 ( 4548) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.381 Fit side-chains revert: symmetry clash REVERT: H 25 SER cc_start: 0.7418 (t) cc_final: 0.7100 (m) REVERT: H 60 TYR cc_start: 0.8189 (m-80) cc_final: 0.7856 (m-10) REVERT: L 62 PHE cc_start: 0.7965 (OUTLIER) cc_final: 0.7031 (p90) REVERT: L 79 GLN cc_start: 0.8532 (mp10) cc_final: 0.8066 (mp10) REVERT: R 386 LYS cc_start: 0.4318 (pttt) cc_final: 0.3107 (pttt) REVERT: R 387 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8043 (tt) REVERT: R 453 TYR cc_start: 0.8650 (p90) cc_final: 0.8447 (p90) REVERT: R 493 GLN cc_start: 0.7930 (tm-30) cc_final: 0.7458 (tm-30) outliers start: 16 outliers final: 12 residues processed: 101 average time/residue: 0.1537 time to fit residues: 18.8503 Evaluate side-chains 106 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain R residue 345 THR Chi-restraints excluded: chain R residue 387 LEU Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 472 ILE Chi-restraints excluded: chain R residue 478 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 5 optimal weight: 0.0980 chunk 12 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 437 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.148223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.125684 restraints weight = 4956.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.126433 restraints weight = 3886.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.127407 restraints weight = 3546.211| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.4205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 3353 Z= 0.233 Angle : 0.833 7.956 4567 Z= 0.421 Chirality : 0.050 0.186 487 Planarity : 0.007 0.076 581 Dihedral : 7.677 48.567 515 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.70 % Favored : 89.30 % Rotamer: Outliers : 5.14 % Allowed : 26.29 % Favored : 68.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.60 (0.38), residues: 402 helix: -3.63 (0.99), residues: 18 sheet: -2.53 (0.41), residues: 130 loop : -2.27 (0.36), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.079 0.004 TRP H 109 HIS 0.001 0.001 HIS L 34 PHE 0.033 0.002 PHE H 106 TYR 0.027 0.002 TYR H 105 ARG 0.007 0.001 ARG R 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00601 ( 1) link_NAG-ASN : angle 0.77063 ( 3) link_BETA1-4 : bond 0.00938 ( 2) link_BETA1-4 : angle 4.24683 ( 6) hydrogen bonds : bond 0.03655 ( 63) hydrogen bonds : angle 5.90755 ( 171) SS BOND : bond 0.00152 ( 5) SS BOND : angle 1.45780 ( 10) covalent geometry : bond 0.00545 ( 3345) covalent geometry : angle 0.81727 ( 4548) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1788.22 seconds wall clock time: 31 minutes 30.32 seconds (1890.32 seconds total)