Starting phenix.real_space_refine on Wed Sep 17 07:43:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9h6u_51901/09_2025/9h6u_51901_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9h6u_51901/09_2025/9h6u_51901.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9h6u_51901/09_2025/9h6u_51901_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9h6u_51901/09_2025/9h6u_51901_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9h6u_51901/09_2025/9h6u_51901.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9h6u_51901/09_2025/9h6u_51901.map" } resolution = 3.27 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 ------------------------------------------------------------------------------- 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= 0.004 sd= 0.091 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: 5 Type Number sf(0) Gaussians S 15 5.16 5 C 2116 2.51 5 N 564 2.21 5 O 654 1.98 5 H 3160 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6509 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 3001 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "H" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1934 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "L" Number of atoms: 1560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 1560 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 8, 'TRANS': 102} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.47, per 1000 atoms: 0.23 Number of scatterers: 6509 At special positions: 0 Unit cell: (59.84, 89.76, 85.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 15 16.00 O 654 8.00 N 564 7.00 C 2116 6.00 H 3160 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.06 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 40 " - pdb=" SG CYS H 114 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 92 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 343 " Time building additional restraints: 0.49 Conformation dependent library (CDL) restraints added in 266.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 780 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 11 sheets defined 13.8% alpha, 33.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.808A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.547A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.603A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.786A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.910A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'H' and resid 105 through 109 Processing helix chain 'L' and resid 29 through 34 Processing helix chain 'L' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.885A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'H' and resid 23 through 24 removed outlier: 3.541A pdb=" N THR H 96 " --> pdb=" O ASP H 91 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 28 through 30 removed outlier: 6.592A pdb=" N ILE H 52 " --> pdb=" O THR H 68 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N THR H 68 " --> pdb=" O ILE H 52 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N TRP H 54 " --> pdb=" O MET H 66 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 28 through 30 Processing sheet with id=AA8, first strand: chain 'H' and resid 122 through 123 Processing sheet with id=AA9, first strand: chain 'L' and resid 11 through 14 removed outlier: 6.571A pdb=" N TRP L 39 " --> pdb=" O LEU L 51 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 11 through 14 Processing sheet with id=AB2, first strand: chain 'L' and resid 20 through 25 130 hydrogen bonds defined for protein. 279 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: 1.45 Time building geometry restraints manager: 0.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.86 - 1.05: 839 1.05 - 1.24: 2795 1.24 - 1.43: 1088 1.43 - 1.62: 1858 1.62 - 1.82: 18 Bond restraints: 6598 Sorted by residual: bond pdb=" N HIS A 519 " pdb=" H HIS A 519 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N GLN H 140 " pdb=" H GLN H 140 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N ASP A 405 " pdb=" H ASP A 405 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N VAL A 445 " pdb=" H VAL A 445 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N THR A 478 " pdb=" H THR A 478 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 ... (remaining 6593 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 9222 2.12 - 4.24: 2052 4.24 - 6.36: 356 6.36 - 8.47: 185 8.47 - 10.59: 3 Bond angle restraints: 11818 Sorted by residual: angle pdb=" N ARG H 116 " pdb=" CA ARG H 116 " pdb=" C ARG H 116 " ideal model delta sigma weight residual 109.23 119.82 -10.59 1.55e+00 4.16e-01 4.67e+01 angle pdb=" OE1 GLN L 93 " pdb=" CD GLN L 93 " pdb=" NE2 GLN L 93 " ideal model delta sigma weight residual 122.60 117.29 5.31 1.00e+00 1.00e+00 2.82e+01 angle pdb=" CA ASP H 124 " pdb=" CB ASP H 124 " pdb=" CG ASP H 124 " ideal model delta sigma weight residual 112.60 117.78 -5.18 1.00e+00 1.00e+00 2.68e+01 angle pdb=" CA ASP A 467 " pdb=" CB ASP A 467 " pdb=" CG ASP A 467 " ideal model delta sigma weight residual 112.60 117.70 -5.10 1.00e+00 1.00e+00 2.61e+01 angle pdb=" CB HIS L 38 " pdb=" CG HIS L 38 " pdb=" CD2 HIS L 38 " ideal model delta sigma weight residual 131.20 124.70 6.50 1.30e+00 5.92e-01 2.50e+01 ... (remaining 11813 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 2916 17.47 - 34.94: 157 34.94 - 52.41: 69 52.41 - 69.88: 72 69.88 - 87.35: 3 Dihedral angle restraints: 3217 sinusoidal: 1707 harmonic: 1510 Sorted by residual: dihedral pdb=" C ASN L 30 " pdb=" N ASN L 30 " pdb=" CA ASN L 30 " pdb=" CB ASN L 30 " ideal model delta harmonic sigma weight residual -122.60 -134.79 12.19 0 2.50e+00 1.60e-01 2.38e+01 dihedral pdb=" CA TYR H 113 " pdb=" C TYR H 113 " pdb=" N CYS H 114 " pdb=" CA CYS H 114 " ideal model delta harmonic sigma weight residual 180.00 156.15 23.85 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" CA LEU A 461 " pdb=" C LEU A 461 " pdb=" N LYS A 462 " pdb=" CA LYS A 462 " ideal model delta harmonic sigma weight residual 180.00 156.30 23.70 0 5.00e+00 4.00e-02 2.25e+01 ... (remaining 3214 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 299 0.078 - 0.156: 153 0.156 - 0.235: 37 0.235 - 0.313: 6 0.313 - 0.391: 2 Chirality restraints: 497 Sorted by residual: chirality pdb=" CA ASN L 30 " pdb=" N ASN L 30 " pdb=" C ASN L 30 " pdb=" CB ASN L 30 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.82e+00 chirality pdb=" CA ASN A 487 " pdb=" N ASN A 487 " pdb=" C ASN A 487 " pdb=" CB ASN A 487 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" CA PHE A 464 " pdb=" N PHE A 464 " pdb=" C PHE A 464 " pdb=" CB PHE A 464 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 494 not shown) Planarity restraints: 1018 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR H 112 " -0.088 2.00e-02 2.50e+03 4.83e-02 7.01e+01 pdb=" CG TYR H 112 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 TYR H 112 " 0.060 2.00e-02 2.50e+03 pdb=" CD2 TYR H 112 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR H 112 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR H 112 " 0.038 2.00e-02 2.50e+03 pdb=" CZ TYR H 112 " 0.014 2.00e-02 2.50e+03 pdb=" OH TYR H 112 " -0.051 2.00e-02 2.50e+03 pdb=" HD1 TYR H 112 " 0.068 2.00e-02 2.50e+03 pdb=" HD2 TYR H 112 " -0.026 2.00e-02 2.50e+03 pdb=" HE1 TYR H 112 " -0.077 2.00e-02 2.50e+03 pdb=" HE2 TYR H 112 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 90 " 0.101 2.00e-02 2.50e+03 4.73e-02 6.72e+01 pdb=" CG TYR L 90 " -0.005 2.00e-02 2.50e+03 pdb=" CD1 TYR L 90 " -0.045 2.00e-02 2.50e+03 pdb=" CD2 TYR L 90 " -0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR L 90 " -0.024 2.00e-02 2.50e+03 pdb=" CE2 TYR L 90 " -0.025 2.00e-02 2.50e+03 pdb=" CZ TYR L 90 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR L 90 " 0.097 2.00e-02 2.50e+03 pdb=" HD1 TYR L 90 " -0.040 2.00e-02 2.50e+03 pdb=" HD2 TYR L 90 " -0.006 2.00e-02 2.50e+03 pdb=" HE1 TYR L 90 " 0.006 2.00e-02 2.50e+03 pdb=" HE2 TYR L 90 " -0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN L 8 " 0.003 2.00e-02 2.50e+03 5.98e-02 5.37e+01 pdb=" CD GLN L 8 " -0.033 2.00e-02 2.50e+03 pdb=" OE1 GLN L 8 " 0.045 2.00e-02 2.50e+03 pdb=" NE2 GLN L 8 " -0.111 2.00e-02 2.50e+03 pdb="HE21 GLN L 8 " 0.074 2.00e-02 2.50e+03 pdb="HE22 GLN L 8 " 0.024 2.00e-02 2.50e+03 ... (remaining 1015 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 443 2.20 - 2.80: 11100 2.80 - 3.40: 17088 3.40 - 4.00: 23455 4.00 - 4.60: 33962 Nonbonded interactions: 86048 Sorted by model distance: nonbonded pdb=" OD1 ASP L 96 " pdb=" HG SER L 98 " model vdw 1.596 2.450 nonbonded pdb=" OD2 ASP H 91 " pdb=" HH TYR H 98 " model vdw 1.605 2.450 nonbonded pdb=" HG SER H 48 " pdb=" OE1 GLU H 92 " model vdw 1.609 2.450 nonbonded pdb=" HG SER A 438 " pdb=" OD2 ASP A 442 " model vdw 1.624 2.450 nonbonded pdb=" OE1 GLU A 406 " pdb=" HH TYR A 495 " model vdw 1.638 2.450 ... (remaining 86043 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 individual isotropic 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: 1.830 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: 0.040 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.110 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 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 : 0.014 0.074 3445 Z= 0.834 Angle : 1.843 10.592 4693 Z= 1.229 Chirality : 0.095 0.391 497 Planarity : 0.010 0.054 611 Dihedral : 11.245 87.346 1233 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 0.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Cbeta Deviations : 0.51 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.12 (0.39), residues: 428 helix: -5.04 (0.27), residues: 20 sheet: 1.57 (0.47), residues: 116 loop : -0.15 (0.34), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 105 TYR 0.090 0.016 TYR L 90 PHE 0.037 0.009 PHE A 338 TRP 0.061 0.014 TRP H 54 HIS 0.012 0.003 HIS L 38 Details of bonding type rmsd covalent geometry : bond 0.01379 ( 3438) covalent geometry : angle 1.83982 ( 4678) SS BOND : bond 0.01202 ( 6) SS BOND : angle 1.79624 ( 12) hydrogen bonds : bond 0.16735 ( 118) hydrogen bonds : angle 9.13470 ( 279) link_NAG-ASN : bond 0.01034 ( 1) link_NAG-ASN : angle 4.68576 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.2147 time to fit residues: 14.5365 Evaluate side-chains 42 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 21 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.160653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.126921 restraints weight = 9651.464| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.08 r_work: 0.3072 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 3445 Z= 0.161 Angle : 0.626 6.136 4693 Z= 0.338 Chirality : 0.046 0.151 497 Planarity : 0.004 0.039 611 Dihedral : 5.255 21.133 502 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.83 % Allowed : 6.37 % Favored : 92.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.05 (0.40), residues: 428 helix: -4.09 (0.72), residues: 20 sheet: 0.71 (0.42), residues: 153 loop : 0.04 (0.38), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 403 TYR 0.018 0.001 TYR A 369 PHE 0.011 0.001 PHE A 338 TRP 0.008 0.001 TRP A 353 HIS 0.003 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 3438) covalent geometry : angle 0.61851 ( 4678) SS BOND : bond 0.00480 ( 6) SS BOND : angle 1.83467 ( 12) hydrogen bonds : bond 0.04489 ( 118) hydrogen bonds : angle 6.77746 ( 279) link_NAG-ASN : bond 0.00009 ( 1) link_NAG-ASN : angle 1.81268 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.124 Fit side-chains revert: symmetry clash REVERT: H 125 ARG cc_start: 0.7530 (mtp-110) cc_final: 0.7278 (ttm170) outliers start: 3 outliers final: 2 residues processed: 51 average time/residue: 0.2675 time to fit residues: 15.4217 Evaluate side-chains 42 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain L residue 60 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 13 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 14 optimal weight: 0.1980 chunk 38 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 21 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.156362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.122732 restraints weight = 9658.085| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.06 r_work: 0.3029 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3445 Z= 0.128 Angle : 0.548 5.329 4693 Z= 0.290 Chirality : 0.046 0.144 497 Planarity : 0.004 0.038 611 Dihedral : 4.544 17.685 502 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.39 % Allowed : 6.37 % Favored : 92.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.18 (0.40), residues: 428 helix: -4.02 (0.80), residues: 20 sheet: 1.16 (0.42), residues: 151 loop : -0.13 (0.38), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG L 65 TYR 0.015 0.001 TYR A 369 PHE 0.009 0.001 PHE L 104 TRP 0.007 0.001 TRP A 436 HIS 0.001 0.000 HIS L 38 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 3438) covalent geometry : angle 0.53889 ( 4678) SS BOND : bond 0.00592 ( 6) SS BOND : angle 1.92341 ( 12) hydrogen bonds : bond 0.03851 ( 118) hydrogen bonds : angle 6.07921 ( 279) link_NAG-ASN : bond 0.00142 ( 1) link_NAG-ASN : angle 1.65004 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.321 Fit side-chains revert: symmetry clash REVERT: H 125 ARG cc_start: 0.7603 (mtp-110) cc_final: 0.7255 (ttp-170) REVERT: L 65 ARG cc_start: 0.7899 (mtp180) cc_final: 0.7628 (mtm110) outliers start: 5 outliers final: 2 residues processed: 47 average time/residue: 0.2231 time to fit residues: 12.2480 Evaluate side-chains 40 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 38 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain L residue 60 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 37 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 21 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 21 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.153644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.122746 restraints weight = 9716.507| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.89 r_work: 0.2978 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.4066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 3445 Z= 0.168 Angle : 0.604 7.361 4693 Z= 0.317 Chirality : 0.047 0.192 497 Planarity : 0.004 0.043 611 Dihedral : 4.615 19.335 502 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 1.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.66 % Allowed : 7.48 % Favored : 90.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.13 (0.40), residues: 428 helix: -4.20 (0.73), residues: 20 sheet: 0.86 (0.41), residues: 163 loop : -0.35 (0.39), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 346 TYR 0.015 0.001 TYR A 369 PHE 0.009 0.001 PHE A 497 TRP 0.009 0.002 TRP A 353 HIS 0.002 0.001 HIS L 38 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 3438) covalent geometry : angle 0.58771 ( 4678) SS BOND : bond 0.00765 ( 6) SS BOND : angle 2.67111 ( 12) hydrogen bonds : bond 0.04486 ( 118) hydrogen bonds : angle 5.74188 ( 279) link_NAG-ASN : bond 0.00079 ( 1) link_NAG-ASN : angle 1.76312 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.181 Fit side-chains REVERT: H 125 ARG cc_start: 0.7750 (mtp-110) cc_final: 0.7377 (ttm170) outliers start: 6 outliers final: 5 residues processed: 44 average time/residue: 0.2469 time to fit residues: 12.4762 Evaluate side-chains 44 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain H residue 48 SER Chi-restraints excluded: chain H residue 134 ASP Chi-restraints excluded: chain L residue 60 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 34 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 15 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 21 optimal weight: 6.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.157176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.127043 restraints weight = 9650.811| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.85 r_work: 0.2977 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.4396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 3445 Z= 0.172 Angle : 0.617 14.101 4693 Z= 0.318 Chirality : 0.046 0.216 497 Planarity : 0.004 0.042 611 Dihedral : 4.566 17.266 502 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 1.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.39 % Allowed : 7.76 % Favored : 90.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.10 (0.40), residues: 428 helix: -4.32 (0.67), residues: 20 sheet: 0.92 (0.41), residues: 164 loop : -0.35 (0.38), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 346 TYR 0.013 0.001 TYR A 369 PHE 0.007 0.001 PHE A 497 TRP 0.007 0.001 TRP A 353 HIS 0.002 0.000 HIS L 38 Details of bonding type rmsd covalent geometry : bond 0.00446 ( 3438) covalent geometry : angle 0.58966 ( 4678) SS BOND : bond 0.00722 ( 6) SS BOND : angle 3.52276 ( 12) hydrogen bonds : bond 0.04086 ( 118) hydrogen bonds : angle 5.81647 ( 279) link_NAG-ASN : bond 0.00094 ( 1) link_NAG-ASN : angle 1.81474 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.186 Fit side-chains REVERT: H 125 ARG cc_start: 0.7858 (mtp-110) cc_final: 0.7387 (ttm170) outliers start: 5 outliers final: 3 residues processed: 47 average time/residue: 0.1868 time to fit residues: 10.5862 Evaluate side-chains 44 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain L residue 60 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.9980 chunk 16 optimal weight: 0.2980 chunk 34 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.159510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.129594 restraints weight = 9636.707| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.86 r_work: 0.3021 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.4556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 3445 Z= 0.103 Angle : 0.572 11.701 4693 Z= 0.297 Chirality : 0.046 0.240 497 Planarity : 0.004 0.038 611 Dihedral : 4.414 22.116 502 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.39 % Allowed : 7.76 % Favored : 90.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.11 (0.40), residues: 428 helix: -4.35 (0.64), residues: 20 sheet: 1.49 (0.43), residues: 147 loop : -0.39 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 346 TYR 0.013 0.001 TYR A 380 PHE 0.006 0.001 PHE A 377 TRP 0.006 0.001 TRP A 436 HIS 0.001 0.000 HIS H 136 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 3438) covalent geometry : angle 0.54468 ( 4678) SS BOND : bond 0.00484 ( 6) SS BOND : angle 3.39367 ( 12) hydrogen bonds : bond 0.03491 ( 118) hydrogen bonds : angle 5.59852 ( 279) link_NAG-ASN : bond 0.00186 ( 1) link_NAG-ASN : angle 1.54568 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.194 Fit side-chains REVERT: H 125 ARG cc_start: 0.7874 (mtp-110) cc_final: 0.7426 (ttm170) outliers start: 5 outliers final: 4 residues processed: 48 average time/residue: 0.1776 time to fit residues: 10.3183 Evaluate side-chains 46 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain H residue 48 SER Chi-restraints excluded: chain H residue 134 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 9 optimal weight: 0.2980 chunk 2 optimal weight: 4.9990 chunk 4 optimal weight: 0.5980 chunk 37 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 14 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.157294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.126951 restraints weight = 9538.235| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.87 r_work: 0.2987 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.4750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3445 Z= 0.125 Angle : 0.560 11.119 4693 Z= 0.292 Chirality : 0.046 0.230 497 Planarity : 0.004 0.036 611 Dihedral : 4.310 18.869 502 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.83 % Allowed : 9.14 % Favored : 90.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.10 (0.40), residues: 428 helix: -4.38 (0.63), residues: 20 sheet: 1.48 (0.44), residues: 147 loop : -0.40 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 346 TYR 0.012 0.001 TYR A 369 PHE 0.006 0.001 PHE A 377 TRP 0.005 0.001 TRP H 65 HIS 0.001 0.000 HIS L 38 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 3438) covalent geometry : angle 0.54276 ( 4678) SS BOND : bond 0.00834 ( 6) SS BOND : angle 2.67232 ( 12) hydrogen bonds : bond 0.03696 ( 118) hydrogen bonds : angle 5.50880 ( 279) link_NAG-ASN : bond 0.00124 ( 1) link_NAG-ASN : angle 1.67945 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.190 Fit side-chains REVERT: A 467 ASP cc_start: 0.7735 (p0) cc_final: 0.7468 (p0) REVERT: H 83 GLN cc_start: 0.7541 (tt0) cc_final: 0.7288 (tt0) outliers start: 3 outliers final: 3 residues processed: 47 average time/residue: 0.1655 time to fit residues: 9.4831 Evaluate side-chains 48 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain H residue 48 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 19 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 36 optimal weight: 0.0970 chunk 33 optimal weight: 0.2980 chunk 27 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.149969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.115983 restraints weight = 9920.821| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.09 r_work: 0.2915 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.4968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 3445 Z= 0.131 Angle : 0.562 10.835 4693 Z= 0.291 Chirality : 0.046 0.219 497 Planarity : 0.004 0.032 611 Dihedral : 4.268 17.789 502 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.83 % Allowed : 9.70 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.07 (0.40), residues: 428 helix: -4.40 (0.62), residues: 20 sheet: 1.43 (0.44), residues: 147 loop : -0.40 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 346 TYR 0.012 0.001 TYR A 369 PHE 0.006 0.001 PHE A 392 TRP 0.006 0.001 TRP H 65 HIS 0.001 0.000 HIS H 137 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 3438) covalent geometry : angle 0.54249 ( 4678) SS BOND : bond 0.00923 ( 6) SS BOND : angle 2.83076 ( 12) hydrogen bonds : bond 0.03667 ( 118) hydrogen bonds : angle 5.40967 ( 279) link_NAG-ASN : bond 0.00142 ( 1) link_NAG-ASN : angle 1.67931 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.194 Fit side-chains REVERT: A 467 ASP cc_start: 0.7607 (p0) cc_final: 0.7270 (p0) outliers start: 3 outliers final: 2 residues processed: 48 average time/residue: 0.1773 time to fit residues: 10.2304 Evaluate side-chains 48 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 46 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 427 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 25 optimal weight: 0.0980 chunk 16 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.151451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.117350 restraints weight = 9925.623| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.10 r_work: 0.2941 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.5128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 3445 Z= 0.109 Angle : 0.534 10.110 4693 Z= 0.276 Chirality : 0.045 0.202 497 Planarity : 0.004 0.057 611 Dihedral : 4.098 18.593 502 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.55 % Allowed : 10.80 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.18 (0.41), residues: 428 helix: -4.38 (0.62), residues: 20 sheet: 1.52 (0.44), residues: 147 loop : -0.33 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 454 TYR 0.011 0.001 TYR A 369 PHE 0.007 0.001 PHE A 392 TRP 0.006 0.001 TRP A 436 HIS 0.001 0.001 HIS H 137 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 3438) covalent geometry : angle 0.51701 ( 4678) SS BOND : bond 0.00738 ( 6) SS BOND : angle 2.62863 ( 12) hydrogen bonds : bond 0.03288 ( 118) hydrogen bonds : angle 5.30710 ( 279) link_NAG-ASN : bond 0.00176 ( 1) link_NAG-ASN : angle 1.52097 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.187 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 50 average time/residue: 0.1766 time to fit residues: 10.6663 Evaluate side-chains 49 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 47 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 427 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 0.3980 chunk 12 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.156484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.126772 restraints weight = 9617.415| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.85 r_work: 0.2958 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.5238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 3445 Z= 0.131 Angle : 0.562 10.471 4693 Z= 0.292 Chirality : 0.046 0.208 497 Planarity : 0.004 0.048 611 Dihedral : 4.146 18.540 502 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.83 % Allowed : 11.08 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.11 (0.40), residues: 428 helix: -4.38 (0.63), residues: 20 sheet: 1.52 (0.44), residues: 147 loop : -0.42 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 346 TYR 0.012 0.001 TYR A 369 PHE 0.006 0.001 PHE A 497 TRP 0.005 0.001 TRP H 65 HIS 0.001 0.000 HIS L 38 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 3438) covalent geometry : angle 0.54518 ( 4678) SS BOND : bond 0.00850 ( 6) SS BOND : angle 2.65306 ( 12) hydrogen bonds : bond 0.03704 ( 118) hydrogen bonds : angle 5.31825 ( 279) link_NAG-ASN : bond 0.00133 ( 1) link_NAG-ASN : angle 1.71947 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 52 time to evaluate : 0.187 Fit side-chains REVERT: H 77 ASP cc_start: 0.8804 (t0) cc_final: 0.8398 (t70) outliers start: 3 outliers final: 2 residues processed: 54 average time/residue: 0.1668 time to fit residues: 10.9485 Evaluate side-chains 51 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 427 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 37 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.152291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.119150 restraints weight = 9814.949| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.06 r_work: 0.2966 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.5344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 3445 Z= 0.114 Angle : 0.566 12.370 4693 Z= 0.292 Chirality : 0.046 0.229 497 Planarity : 0.004 0.040 611 Dihedral : 4.191 22.350 502 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.83 % Allowed : 10.80 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.13 (0.40), residues: 428 helix: -4.37 (0.62), residues: 20 sheet: 1.52 (0.44), residues: 147 loop : -0.39 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 346 TYR 0.011 0.001 TYR A 369 PHE 0.005 0.001 PHE A 377 TRP 0.006 0.001 TRP A 436 HIS 0.001 0.000 HIS L 38 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 3438) covalent geometry : angle 0.54655 ( 4678) SS BOND : bond 0.00770 ( 6) SS BOND : angle 2.90111 ( 12) hydrogen bonds : bond 0.03454 ( 118) hydrogen bonds : angle 5.43654 ( 279) link_NAG-ASN : bond 0.00174 ( 1) link_NAG-ASN : angle 1.57636 ( 3) =============================================================================== Job complete usr+sys time: 2412.11 seconds wall clock time: 41 minutes 39.39 seconds (2499.39 seconds total)