Starting phenix.real_space_refine on Tue Mar 3 11:37:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7won_32652/03_2026/7won_32652.cif Found real_map, /net/cci-nas-00/data/ceres_data/7won_32652/03_2026/7won_32652.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7won_32652/03_2026/7won_32652.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7won_32652/03_2026/7won_32652.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7won_32652/03_2026/7won_32652.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7won_32652/03_2026/7won_32652.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.010 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 2098 2.51 5 N 556 2.21 5 O 649 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3318 Number of models: 1 Model: "" Number of chains: 4 Chain: "F" Number of atoms: 1462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1462 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 9, 'TRANS': 173} Chain: "L" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 811 Classifications: {'peptide': 111} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "H" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1017 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 128} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 0.90, per 1000 atoms: 0.27 Number of scatterers: 3318 At special positions: 0 Unit cell: (73.132, 84.024, 80.912, 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 649 8.00 N 556 7.00 C 2098 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS F 379 " - pdb=" SG CYS F 432 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " 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 BETA1-4 " NAG A 1 " - " NAG A 2 " NAG-ASN " NAG A 1 " - " ASN F 343 " Time building additional restraints: 0.30 Conformation dependent library (CDL) restraints added in 128.1 milliseconds 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 760 Finding SS restraints... Secondary structure from input PDB file: 1 helices and 8 sheets defined 1.4% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'F' and resid 405 through 410 removed outlier: 4.532A pdb=" N ARG F 408 " --> pdb=" O ASP F 405 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 356 through 358 removed outlier: 3.564A pdb=" N LYS F 356 " --> pdb=" O ALA F 397 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N CYS F 432 " --> pdb=" O LEU F 513 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'L' and resid 17 through 23 removed outlier: 3.501A pdb=" N SER L 69 " --> pdb=" O SER L 72 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER L 74 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 47 through 51 removed outlier: 5.896A pdb=" N LEU L 48 " --> pdb=" O GLN L 39 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N GLN L 39 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 6 through 7 removed outlier: 3.748A pdb=" N SER H 7 " --> pdb=" O SER H 21 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LEU H 18 " --> pdb=" O MET H 83 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET H 83 " --> pdb=" O LEU H 18 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AA7, first strand: chain 'H' and resid 58 through 60 removed outlier: 5.113A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 102 through 104 66 hydrogen bonds defined for protein. 168 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: 0.52 Time building geometry restraints manager: 0.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 538 1.30 - 1.43: 1004 1.43 - 1.56: 1840 1.56 - 1.69: 0 1.69 - 1.82: 19 Bond restraints: 3401 Sorted by residual: bond pdb=" C ARG H 106 " pdb=" N SER H 107 " ideal model delta sigma weight residual 1.332 1.240 0.092 1.40e-02 5.10e+03 4.33e+01 bond pdb=" C ARG H 106 " pdb=" O ARG H 106 " ideal model delta sigma weight residual 1.237 1.171 0.066 1.16e-02 7.43e+03 3.19e+01 bond pdb=" CA ASP H 113 " pdb=" C ASP H 113 " ideal model delta sigma weight residual 1.523 1.453 0.070 1.28e-02 6.10e+03 2.98e+01 bond pdb=" CA ARG H 106 " pdb=" C ARG H 106 " ideal model delta sigma weight residual 1.524 1.477 0.046 1.26e-02 6.30e+03 1.35e+01 bond pdb=" CA ARG H 106 " pdb=" CB ARG H 106 " ideal model delta sigma weight residual 1.529 1.473 0.056 1.58e-02 4.01e+03 1.27e+01 ... (remaining 3396 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.84: 4523 2.84 - 5.69: 80 5.69 - 8.53: 12 8.53 - 11.37: 2 11.37 - 14.22: 3 Bond angle restraints: 4620 Sorted by residual: angle pdb=" N TYR H 103 " pdb=" CA TYR H 103 " pdb=" C TYR H 103 " ideal model delta sigma weight residual 109.52 121.19 -11.67 1.55e+00 4.16e-01 5.67e+01 angle pdb=" O VAL H 100 " pdb=" C VAL H 100 " pdb=" N GLN H 101 " ideal model delta sigma weight residual 122.57 114.38 8.19 1.25e+00 6.40e-01 4.30e+01 angle pdb=" N LEU H 112 " pdb=" CA LEU H 112 " pdb=" C LEU H 112 " ideal model delta sigma weight residual 110.35 101.53 8.82 1.36e+00 5.41e-01 4.21e+01 angle pdb=" C ARG H 106 " pdb=" N SER H 107 " pdb=" CA SER H 107 " ideal model delta sigma weight residual 121.54 109.28 12.26 1.91e+00 2.74e-01 4.12e+01 angle pdb=" CA ARG H 106 " pdb=" C ARG H 106 " pdb=" O ARG H 106 " ideal model delta sigma weight residual 120.70 127.27 -6.57 1.03e+00 9.43e-01 4.06e+01 ... (remaining 4615 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.55: 1823 20.55 - 41.09: 143 41.09 - 61.64: 19 61.64 - 82.18: 6 82.18 - 102.73: 10 Dihedral angle restraints: 2001 sinusoidal: 787 harmonic: 1214 Sorted by residual: dihedral pdb=" CA PHE F 429 " pdb=" C PHE F 429 " pdb=" N THR F 430 " pdb=" CA THR F 430 " ideal model delta harmonic sigma weight residual 180.00 151.21 28.79 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA ASN F 460 " pdb=" C ASN F 460 " pdb=" N LEU F 461 " pdb=" CA LEU F 461 " ideal model delta harmonic sigma weight residual -180.00 -154.65 -25.35 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" CA CYS F 336 " pdb=" C CYS F 336 " pdb=" N PRO F 337 " pdb=" CA PRO F 337 " ideal model delta harmonic sigma weight residual -180.00 -160.93 -19.07 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 1998 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 365 0.059 - 0.119: 101 0.119 - 0.178: 19 0.178 - 0.238: 6 0.238 - 0.297: 1 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA ASP H 113 " pdb=" N ASP H 113 " pdb=" C ASP H 113 " pdb=" CB ASP H 113 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CA TYR H 103 " pdb=" N TYR H 103 " pdb=" C TYR H 103 " pdb=" CB TYR H 103 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" C1 NAG A 1 " pdb=" ND2 ASN F 343 " pdb=" C2 NAG A 1 " pdb=" O5 NAG A 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 489 not shown) Planarity restraints: 601 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL H 100 " 0.042 2.00e-02 2.50e+03 7.95e-02 6.33e+01 pdb=" C VAL H 100 " -0.138 2.00e-02 2.50e+03 pdb=" O VAL H 100 " 0.051 2.00e-02 2.50e+03 pdb=" N GLN H 101 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS F 462 " 0.042 5.00e-02 4.00e+02 6.32e-02 6.39e+00 pdb=" N PRO F 463 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO F 463 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO F 463 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG L 56 " 0.040 5.00e-02 4.00e+02 6.06e-02 5.87e+00 pdb=" N PRO L 57 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO L 57 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO L 57 " 0.033 5.00e-02 4.00e+02 ... (remaining 598 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 50 2.61 - 3.18: 2613 3.18 - 3.75: 4748 3.75 - 4.33: 6402 4.33 - 4.90: 10870 Nonbonded interactions: 24683 Sorted by model distance: nonbonded pdb=" O ARG H 106 " pdb=" C SER H 107 " model vdw 2.035 3.270 nonbonded pdb=" O SER F 371 " pdb=" NH1 ARG H 106 " model vdw 2.238 3.120 nonbonded pdb=" O ASN F 439 " pdb=" OG SER F 443 " model vdw 2.276 3.040 nonbonded pdb=" O ARG H 106 " pdb=" CA SER H 107 " model vdw 2.278 2.776 nonbonded pdb=" OG SER F 349 " pdb=" O LEU F 452 " model vdw 2.302 3.040 ... (remaining 24678 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=0.00 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: 7.360 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: 0.060 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 5.400 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.010 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 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 : 0.006 0.092 3406 Z= 0.359 Angle : 0.978 14.217 4632 Z= 0.563 Chirality : 0.060 0.297 492 Planarity : 0.008 0.080 600 Dihedral : 16.809 102.726 1232 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.79 % Favored : 90.21 % Rotamer: Outliers : 0.28 % Allowed : 10.14 % Favored : 89.58 % 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 are not related in a simple way. whole: -4.42 (0.35), residues: 419 helix: -4.82 (0.44), residues: 14 sheet: -2.40 (0.44), residues: 127 loop : -3.30 (0.30), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 106 TYR 0.021 0.002 TYR H 104 PHE 0.011 0.002 PHE F 400 TRP 0.033 0.002 TRP F 436 HIS 0.006 0.003 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00604 ( 3401) covalent geometry : angle 0.97704 ( 4620) SS BOND : bond 0.00241 ( 3) SS BOND : angle 0.61938 ( 6) hydrogen bonds : bond 0.30355 ( 66) hydrogen bonds : angle 11.76116 ( 168) link_BETA1-4 : bond 0.01260 ( 1) link_BETA1-4 : angle 2.10600 ( 3) link_NAG-ASN : bond 0.00107 ( 1) link_NAG-ASN : angle 0.76846 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 94 time to evaluate : 0.124 Fit side-chains revert: symmetry clash REVERT: F 354 ASN cc_start: 0.8755 (p0) cc_final: 0.8455 (p0) REVERT: F 474 GLN cc_start: 0.6126 (tp40) cc_final: 0.5871 (tm-30) REVERT: L 16 GLN cc_start: 0.8731 (mm110) cc_final: 0.8169 (mp10) REVERT: H 16 ARG cc_start: 0.2340 (mmt180) cc_final: 0.1973 (mmt180) outliers start: 1 outliers final: 1 residues processed: 95 average time/residue: 0.0838 time to fit residues: 9.4356 Evaluate side-chains 77 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 76 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 106 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 0.1980 chunk 22 optimal weight: 0.0770 chunk 37 optimal weight: 0.8980 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 370 ASN F 388 ASN ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 414 GLN F 487 ASN L 6 GLN L 16 GLN L 40 GLN H 13 GLN H 39 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.149227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.123253 restraints weight = 4870.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.127002 restraints weight = 3037.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.129554 restraints weight = 2229.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.131101 restraints weight = 1806.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.132481 restraints weight = 1572.067| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3300 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3299 r_free = 0.3299 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3299 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3406 Z= 0.183 Angle : 0.669 8.205 4632 Z= 0.338 Chirality : 0.047 0.235 492 Planarity : 0.005 0.043 600 Dihedral : 11.872 77.945 522 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.69 % Favored : 88.31 % Rotamer: Outliers : 4.79 % Allowed : 17.18 % Favored : 78.03 % 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 are not related in a simple way. whole: -3.93 (0.38), residues: 419 helix: -4.52 (0.76), residues: 14 sheet: -2.30 (0.44), residues: 132 loop : -2.80 (0.35), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG H 87 TYR 0.015 0.002 TYR F 495 PHE 0.016 0.002 PHE F 338 TRP 0.018 0.002 TRP F 436 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 3401) covalent geometry : angle 0.66678 ( 4620) SS BOND : bond 0.00239 ( 3) SS BOND : angle 0.53580 ( 6) hydrogen bonds : bond 0.04888 ( 66) hydrogen bonds : angle 8.01927 ( 168) link_BETA1-4 : bond 0.01152 ( 1) link_BETA1-4 : angle 2.47278 ( 3) link_NAG-ASN : bond 0.00184 ( 1) link_NAG-ASN : angle 0.69176 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.116 Fit side-chains REVERT: F 354 ASN cc_start: 0.8892 (p0) cc_final: 0.8576 (p0) REVERT: F 427 ASP cc_start: 0.8208 (OUTLIER) cc_final: 0.7995 (t0) REVERT: F 474 GLN cc_start: 0.6068 (tp40) cc_final: 0.5750 (tm-30) REVERT: L 6 GLN cc_start: 0.8963 (OUTLIER) cc_final: 0.8714 (pt0) REVERT: L 16 GLN cc_start: 0.8663 (mm-40) cc_final: 0.8077 (mp10) REVERT: H 16 ARG cc_start: 0.2214 (mmt180) cc_final: 0.1899 (mmt180) REVERT: H 114 TYR cc_start: 0.7888 (m-80) cc_final: 0.7642 (m-80) outliers start: 17 outliers final: 10 residues processed: 97 average time/residue: 0.0785 time to fit residues: 8.9037 Evaluate side-chains 91 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 402 ILE Chi-restraints excluded: chain F residue 427 ASP Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 51 TYR Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain H residue 126 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 18 optimal weight: 0.0370 chunk 24 optimal weight: 2.9990 chunk 17 optimal weight: 0.0870 chunk 32 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 22 optimal weight: 0.0040 chunk 26 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.3248 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 409 GLN F 422 ASN L 6 GLN L 91 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.137381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.115876 restraints weight = 4990.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.118732 restraints weight = 3298.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.120709 restraints weight = 2488.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.121969 restraints weight = 2044.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.123094 restraints weight = 1787.104| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3406 Z= 0.127 Angle : 0.640 9.262 4632 Z= 0.314 Chirality : 0.046 0.242 492 Planarity : 0.004 0.038 600 Dihedral : 10.249 66.142 518 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 2.54 % Allowed : 20.85 % Favored : 76.62 % 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 are not related in a simple way. whole: -3.56 (0.39), residues: 419 helix: -4.65 (0.65), residues: 14 sheet: -1.98 (0.45), residues: 133 loop : -2.56 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 19 TYR 0.013 0.001 TYR F 369 PHE 0.010 0.001 PHE F 338 TRP 0.011 0.001 TRP F 436 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 3401) covalent geometry : angle 0.63689 ( 4620) SS BOND : bond 0.00254 ( 3) SS BOND : angle 0.55291 ( 6) hydrogen bonds : bond 0.04178 ( 66) hydrogen bonds : angle 7.08968 ( 168) link_BETA1-4 : bond 0.00937 ( 1) link_BETA1-4 : angle 2.72317 ( 3) link_NAG-ASN : bond 0.00008 ( 1) link_NAG-ASN : angle 0.49164 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.096 Fit side-chains revert: symmetry clash REVERT: F 354 ASN cc_start: 0.8838 (p0) cc_final: 0.8517 (p0) REVERT: F 474 GLN cc_start: 0.5858 (tp40) cc_final: 0.5332 (tm-30) REVERT: L 16 GLN cc_start: 0.8553 (mm-40) cc_final: 0.8103 (mp10) REVERT: H 16 ARG cc_start: 0.2425 (mmt180) cc_final: 0.0282 (mmt180) outliers start: 9 outliers final: 7 residues processed: 85 average time/residue: 0.0882 time to fit residues: 8.7662 Evaluate side-chains 85 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 51 TYR Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 91 GLN Chi-restraints excluded: chain H residue 113 ASP Chi-restraints excluded: chain H residue 126 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 16 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 32 optimal weight: 0.2980 chunk 23 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3498 r_free = 0.3498 target = 0.134905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.113326 restraints weight = 4993.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.116015 restraints weight = 3319.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.117823 restraints weight = 2527.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.119209 restraints weight = 2100.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.119931 restraints weight = 1836.378| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3406 Z= 0.181 Angle : 0.663 9.464 4632 Z= 0.324 Chirality : 0.047 0.232 492 Planarity : 0.004 0.033 600 Dihedral : 9.148 56.750 518 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.22 % Favored : 88.78 % Rotamer: Outliers : 4.79 % Allowed : 19.72 % Favored : 75.49 % 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 are not related in a simple way. whole: -3.44 (0.40), residues: 419 helix: -4.60 (0.69), residues: 14 sheet: -1.90 (0.46), residues: 133 loop : -2.47 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 346 TYR 0.020 0.002 TYR H 114 PHE 0.014 0.002 PHE F 338 TRP 0.016 0.001 TRP F 436 HIS 0.004 0.002 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00420 ( 3401) covalent geometry : angle 0.65818 ( 4620) SS BOND : bond 0.00239 ( 3) SS BOND : angle 0.77150 ( 6) hydrogen bonds : bond 0.04166 ( 66) hydrogen bonds : angle 6.65913 ( 168) link_BETA1-4 : bond 0.01088 ( 1) link_BETA1-4 : angle 3.05475 ( 3) link_NAG-ASN : bond 0.00123 ( 1) link_NAG-ASN : angle 0.68578 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.101 Fit side-chains REVERT: F 354 ASN cc_start: 0.8891 (p0) cc_final: 0.8552 (p0) REVERT: F 474 GLN cc_start: 0.5944 (tp40) cc_final: 0.5350 (tm-30) REVERT: L 16 GLN cc_start: 0.8617 (mm-40) cc_final: 0.8116 (mp10) REVERT: H 16 ARG cc_start: 0.2306 (mmt180) cc_final: 0.1947 (mmt180) REVERT: H 113 ASP cc_start: 0.8857 (OUTLIER) cc_final: 0.8465 (m-30) outliers start: 17 outliers final: 12 residues processed: 91 average time/residue: 0.0675 time to fit residues: 7.3486 Evaluate side-chains 87 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 51 TYR Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 113 ASP Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 127 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 23 optimal weight: 0.0670 overall best weight: 0.8122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 40 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.131704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.109359 restraints weight = 5033.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.112050 restraints weight = 3387.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.113956 restraints weight = 2595.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.115154 restraints weight = 2153.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.116209 restraints weight = 1898.609| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 3406 Z= 0.221 Angle : 0.698 9.711 4632 Z= 0.344 Chirality : 0.048 0.211 492 Planarity : 0.004 0.033 600 Dihedral : 8.569 56.248 518 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.69 % Favored : 88.31 % Rotamer: Outliers : 4.79 % Allowed : 21.69 % Favored : 73.52 % 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 are not related in a simple way. whole: -3.42 (0.40), residues: 419 helix: -4.69 (0.60), residues: 14 sheet: -1.93 (0.46), residues: 133 loop : -2.42 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 72 TYR 0.028 0.002 TYR H 114 PHE 0.021 0.002 PHE F 347 TRP 0.021 0.002 TRP F 436 HIS 0.005 0.002 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00511 ( 3401) covalent geometry : angle 0.69273 ( 4620) SS BOND : bond 0.00238 ( 3) SS BOND : angle 0.71975 ( 6) hydrogen bonds : bond 0.04372 ( 66) hydrogen bonds : angle 6.64851 ( 168) link_BETA1-4 : bond 0.01134 ( 1) link_BETA1-4 : angle 3.18826 ( 3) link_NAG-ASN : bond 0.00189 ( 1) link_NAG-ASN : angle 1.02537 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.106 Fit side-chains REVERT: F 354 ASN cc_start: 0.8910 (p0) cc_final: 0.8595 (p0) REVERT: F 474 GLN cc_start: 0.6004 (tp40) cc_final: 0.5359 (tm-30) REVERT: L 16 GLN cc_start: 0.8640 (mm-40) cc_final: 0.8164 (mp10) REVERT: H 16 ARG cc_start: 0.2305 (mmt180) cc_final: 0.1910 (mmt180) REVERT: H 53 PHE cc_start: 0.7605 (OUTLIER) cc_final: 0.7142 (t80) outliers start: 17 outliers final: 12 residues processed: 92 average time/residue: 0.0853 time to fit residues: 9.1687 Evaluate side-chains 91 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 51 TYR Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain H residue 53 PHE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 127 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 16 optimal weight: 0.0570 chunk 15 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 35 optimal weight: 0.0770 chunk 23 optimal weight: 0.3980 chunk 28 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 overall best weight: 0.3456 ------------------------------------------------------------------------------- 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 = 0.3511 r_free = 0.3511 target = 0.136762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.114538 restraints weight = 4995.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.117321 restraints weight = 3343.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.119329 restraints weight = 2537.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.120716 restraints weight = 2088.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.121536 restraints weight = 1821.279| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3406 Z= 0.124 Angle : 0.640 10.011 4632 Z= 0.310 Chirality : 0.046 0.219 492 Planarity : 0.004 0.033 600 Dihedral : 7.792 59.978 518 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 3.10 % Allowed : 24.23 % Favored : 72.68 % 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 are not related in a simple way. whole: -3.15 (0.40), residues: 419 helix: -4.92 (0.45), residues: 20 sheet: -1.66 (0.48), residues: 127 loop : -2.17 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 72 TYR 0.028 0.001 TYR H 114 PHE 0.009 0.001 PHE F 456 TRP 0.010 0.001 TRP F 436 HIS 0.005 0.002 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 3401) covalent geometry : angle 0.63432 ( 4620) SS BOND : bond 0.00332 ( 3) SS BOND : angle 0.88811 ( 6) hydrogen bonds : bond 0.03459 ( 66) hydrogen bonds : angle 6.34715 ( 168) link_BETA1-4 : bond 0.01044 ( 1) link_BETA1-4 : angle 3.08829 ( 3) link_NAG-ASN : bond 0.00099 ( 1) link_NAG-ASN : angle 1.22059 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.112 Fit side-chains REVERT: F 354 ASN cc_start: 0.8824 (p0) cc_final: 0.8496 (p0) REVERT: F 474 GLN cc_start: 0.5876 (tp40) cc_final: 0.5351 (tm-30) REVERT: L 16 GLN cc_start: 0.8603 (mm-40) cc_final: 0.8109 (mp10) REVERT: H 16 ARG cc_start: 0.2760 (mmt180) cc_final: 0.0538 (mmt180) REVERT: H 25 SER cc_start: 0.9333 (t) cc_final: 0.9020 (m) REVERT: H 53 PHE cc_start: 0.7514 (OUTLIER) cc_final: 0.7248 (t80) REVERT: H 113 ASP cc_start: 0.8808 (OUTLIER) cc_final: 0.8401 (m-30) outliers start: 11 outliers final: 9 residues processed: 90 average time/residue: 0.0750 time to fit residues: 8.1058 Evaluate side-chains 89 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 495 TYR Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain H residue 53 PHE Chi-restraints excluded: chain H residue 113 ASP Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 126 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 0 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 30 optimal weight: 0.0370 chunk 21 optimal weight: 0.2980 chunk 19 optimal weight: 3.9990 chunk 22 optimal weight: 0.0170 chunk 40 optimal weight: 0.9980 chunk 9 optimal weight: 0.0970 chunk 27 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 overall best weight: 0.2294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 40 GLN H 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.137228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.115073 restraints weight = 4973.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.117937 restraints weight = 3273.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.119991 restraints weight = 2456.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.121255 restraints weight = 2002.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.122290 restraints weight = 1749.613| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3406 Z= 0.109 Angle : 0.633 9.469 4632 Z= 0.305 Chirality : 0.046 0.248 492 Planarity : 0.004 0.032 600 Dihedral : 6.951 55.614 518 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 3.66 % Allowed : 24.51 % Favored : 71.83 % 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 are not related in a simple way. whole: -3.00 (0.41), residues: 419 helix: -4.98 (0.39), residues: 20 sheet: -1.41 (0.49), residues: 128 loop : -2.14 (0.37), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 72 TYR 0.023 0.001 TYR H 114 PHE 0.009 0.001 PHE F 456 TRP 0.008 0.001 TRP H 47 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 3401) covalent geometry : angle 0.62596 ( 4620) SS BOND : bond 0.00246 ( 3) SS BOND : angle 1.16157 ( 6) hydrogen bonds : bond 0.03245 ( 66) hydrogen bonds : angle 6.09814 ( 168) link_BETA1-4 : bond 0.01111 ( 1) link_BETA1-4 : angle 3.09671 ( 3) link_NAG-ASN : bond 0.00207 ( 1) link_NAG-ASN : angle 1.56647 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.157 Fit side-chains REVERT: F 354 ASN cc_start: 0.8818 (p0) cc_final: 0.8478 (p0) REVERT: F 474 GLN cc_start: 0.5827 (tp40) cc_final: 0.5352 (tm-30) REVERT: L 16 GLN cc_start: 0.8571 (mm-40) cc_final: 0.8074 (mp10) REVERT: H 16 ARG cc_start: 0.2436 (mmt180) cc_final: -0.0555 (mpt180) REVERT: H 25 SER cc_start: 0.9315 (t) cc_final: 0.9012 (m) REVERT: H 113 ASP cc_start: 0.8722 (OUTLIER) cc_final: 0.8302 (m-30) outliers start: 13 outliers final: 10 residues processed: 92 average time/residue: 0.0718 time to fit residues: 7.8761 Evaluate side-chains 88 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain F residue 495 TYR Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain H residue 113 ASP Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 126 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 37 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 3 optimal weight: 0.4980 chunk 38 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 22 optimal weight: 0.1980 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 40 GLN H 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.135894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.113860 restraints weight = 5110.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.116689 restraints weight = 3346.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.118705 restraints weight = 2514.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.119943 restraints weight = 2057.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.120692 restraints weight = 1801.249| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3406 Z= 0.170 Angle : 0.675 9.062 4632 Z= 0.326 Chirality : 0.047 0.246 492 Planarity : 0.004 0.031 600 Dihedral : 6.940 53.076 518 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.26 % Favored : 89.74 % Rotamer: Outliers : 4.23 % Allowed : 24.79 % Favored : 70.99 % 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 are not related in a simple way. whole: -3.02 (0.40), residues: 419 helix: -4.91 (0.44), residues: 20 sheet: -1.48 (0.47), residues: 133 loop : -2.13 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 346 TYR 0.020 0.002 TYR H 114 PHE 0.013 0.002 PHE F 347 TRP 0.017 0.001 TRP F 436 HIS 0.005 0.002 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 3401) covalent geometry : angle 0.66860 ( 4620) SS BOND : bond 0.00261 ( 3) SS BOND : angle 1.33316 ( 6) hydrogen bonds : bond 0.03654 ( 66) hydrogen bonds : angle 6.14291 ( 168) link_BETA1-4 : bond 0.01181 ( 1) link_BETA1-4 : angle 3.13901 ( 3) link_NAG-ASN : bond 0.00038 ( 1) link_NAG-ASN : angle 1.48206 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.127 Fit side-chains REVERT: F 354 ASN cc_start: 0.8826 (p0) cc_final: 0.8489 (p0) REVERT: F 474 GLN cc_start: 0.5893 (tp40) cc_final: 0.5384 (tm-30) REVERT: L 16 GLN cc_start: 0.8608 (mm-40) cc_final: 0.8084 (mp10) REVERT: H 16 ARG cc_start: 0.2548 (mmt180) cc_final: 0.2128 (mmt180) outliers start: 15 outliers final: 13 residues processed: 84 average time/residue: 0.0797 time to fit residues: 7.9592 Evaluate side-chains 86 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain F residue 495 TYR Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain H residue 53 PHE Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 126 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 28 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 5 optimal weight: 0.0270 chunk 14 optimal weight: 0.0030 chunk 38 optimal weight: 0.8980 chunk 18 optimal weight: 0.4980 chunk 36 optimal weight: 0.0070 chunk 21 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 overall best weight: 0.2266 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 40 GLN H 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.137861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.116893 restraints weight = 4990.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.119317 restraints weight = 3525.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.120972 restraints weight = 2768.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.121898 restraints weight = 2336.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.122835 restraints weight = 2094.840| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3406 Z= 0.110 Angle : 0.637 9.094 4632 Z= 0.303 Chirality : 0.046 0.241 492 Planarity : 0.004 0.032 600 Dihedral : 6.501 50.400 518 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 3.10 % Allowed : 25.35 % Favored : 71.55 % 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 are not related in a simple way. whole: -2.87 (0.40), residues: 419 helix: -4.91 (0.44), residues: 20 sheet: -1.31 (0.48), residues: 128 loop : -2.05 (0.37), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 346 TYR 0.015 0.001 TYR H 114 PHE 0.009 0.001 PHE F 456 TRP 0.008 0.001 TRP H 36 HIS 0.005 0.002 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 3401) covalent geometry : angle 0.63009 ( 4620) SS BOND : bond 0.00331 ( 3) SS BOND : angle 1.11762 ( 6) hydrogen bonds : bond 0.03169 ( 66) hydrogen bonds : angle 6.03857 ( 168) link_BETA1-4 : bond 0.01096 ( 1) link_BETA1-4 : angle 3.04359 ( 3) link_NAG-ASN : bond 0.00182 ( 1) link_NAG-ASN : angle 1.55557 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.117 Fit side-chains REVERT: F 354 ASN cc_start: 0.8780 (p0) cc_final: 0.8431 (p0) REVERT: F 474 GLN cc_start: 0.5814 (tp40) cc_final: 0.5346 (tm-30) REVERT: L 16 GLN cc_start: 0.8609 (mm-40) cc_final: 0.8093 (mp10) REVERT: H 16 ARG cc_start: 0.2530 (mmt180) cc_final: -0.0480 (mpt180) REVERT: H 25 SER cc_start: 0.9293 (t) cc_final: 0.9002 (m) outliers start: 11 outliers final: 9 residues processed: 83 average time/residue: 0.0717 time to fit residues: 7.0994 Evaluate side-chains 85 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 495 TYR Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain H residue 53 PHE Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 126 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 38 optimal weight: 0.3980 chunk 19 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 40 GLN H 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.132562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.111571 restraints weight = 5041.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.113866 restraints weight = 3579.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.115620 restraints weight = 2810.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.116665 restraints weight = 2364.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.117172 restraints weight = 2111.868| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 3406 Z= 0.197 Angle : 0.695 9.389 4632 Z= 0.338 Chirality : 0.048 0.247 492 Planarity : 0.004 0.030 600 Dihedral : 6.811 50.843 518 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.26 % Favored : 89.74 % Rotamer: Outliers : 2.54 % Allowed : 26.48 % Favored : 70.99 % 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 are not related in a simple way. whole: -2.88 (0.41), residues: 419 helix: -4.90 (0.45), residues: 20 sheet: -1.28 (0.48), residues: 126 loop : -2.07 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 346 TYR 0.017 0.002 TYR H 114 PHE 0.015 0.002 PHE F 338 TRP 0.018 0.002 TRP F 436 HIS 0.005 0.002 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00458 ( 3401) covalent geometry : angle 0.68895 ( 4620) SS BOND : bond 0.00270 ( 3) SS BOND : angle 1.12981 ( 6) hydrogen bonds : bond 0.03798 ( 66) hydrogen bonds : angle 6.10464 ( 168) link_BETA1-4 : bond 0.01113 ( 1) link_BETA1-4 : angle 3.06389 ( 3) link_NAG-ASN : bond 0.00032 ( 1) link_NAG-ASN : angle 1.49165 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.129 Fit side-chains REVERT: F 354 ASN cc_start: 0.8830 (p0) cc_final: 0.8478 (p0) REVERT: F 474 GLN cc_start: 0.5920 (tp40) cc_final: 0.5365 (tm-30) REVERT: L 16 GLN cc_start: 0.8616 (mm-40) cc_final: 0.8096 (mp10) REVERT: L 93 TYR cc_start: 0.8073 (t80) cc_final: 0.7860 (t80) REVERT: H 16 ARG cc_start: 0.2462 (mmt180) cc_final: 0.2023 (mmt180) outliers start: 9 outliers final: 8 residues processed: 81 average time/residue: 0.0801 time to fit residues: 7.6381 Evaluate side-chains 83 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 495 TYR Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain H residue 53 PHE Chi-restraints excluded: chain H residue 126 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 17 optimal weight: 0.1980 chunk 35 optimal weight: 0.7980 chunk 8 optimal weight: 0.0070 chunk 2 optimal weight: 0.0670 chunk 24 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 33 optimal weight: 0.2980 chunk 29 optimal weight: 1.9990 overall best weight: 0.2336 ------------------------------------------------------------------------------- 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 = 0.3544 r_free = 0.3544 target = 0.139810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.117573 restraints weight = 5090.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.120593 restraints weight = 3303.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.122495 restraints weight = 2468.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.124132 restraints weight = 2024.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.124891 restraints weight = 1741.507| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3406 Z= 0.112 Angle : 0.643 9.504 4632 Z= 0.307 Chirality : 0.046 0.238 492 Planarity : 0.004 0.033 600 Dihedral : 6.329 48.316 518 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 2.54 % Allowed : 26.76 % Favored : 70.70 % 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 are not related in a simple way. whole: -2.70 (0.41), residues: 419 helix: -4.91 (0.43), residues: 20 sheet: -1.19 (0.48), residues: 132 loop : -1.92 (0.38), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 346 TYR 0.011 0.001 TYR F 369 PHE 0.008 0.001 PHE F 456 TRP 0.007 0.001 TRP F 436 HIS 0.004 0.002 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 3401) covalent geometry : angle 0.63703 ( 4620) SS BOND : bond 0.00270 ( 3) SS BOND : angle 0.92092 ( 6) hydrogen bonds : bond 0.03141 ( 66) hydrogen bonds : angle 5.98405 ( 168) link_BETA1-4 : bond 0.01040 ( 1) link_BETA1-4 : angle 2.90001 ( 3) link_NAG-ASN : bond 0.00187 ( 1) link_NAG-ASN : angle 1.54749 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 994.45 seconds wall clock time: 17 minutes 38.15 seconds (1058.15 seconds total)