Starting phenix.real_space_refine on Thu Jul 24 03:01:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mlz_23914/07_2025/7mlz_23914.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mlz_23914/07_2025/7mlz_23914.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mlz_23914/07_2025/7mlz_23914.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mlz_23914/07_2025/7mlz_23914.map" model { file = "/net/cci-nas-00/data/ceres_data/7mlz_23914/07_2025/7mlz_23914.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mlz_23914/07_2025/7mlz_23914.cif" } resolution = 3.71 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.006 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 22 5.16 5 C 3073 2.51 5 N 809 2.21 5 O 960 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 4864 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1551 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 11, 'TRANS': 184} Chain: "H" Number of atoms: 1611 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 215, 1611 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "L" Number of atoms: 1641 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 213, 1641 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 200} Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 5.86, per 1000 atoms: 1.20 Number of scatterers: 4864 At special positions: 0 Unit cell: (86.427, 61.983, 138.807, 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 22 16.00 O 960 8.00 N 809 7.00 C 3073 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS H 97 " - pdb=" SG CYS H 100B" distance=2.04 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS H 196 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " 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 ALPHA1-3 " BMA B 3 " - " MAN B 4 " ALPHA1-6 " BMA B 3 " - " MAN B 5 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " NAG-ASN " NAG B 1 " - " ASN A 343 " Time building additional restraints: 2.42 Conformation dependent library (CDL) restraints added in 707.5 milliseconds 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1152 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 14 sheets defined 5.0% alpha, 18.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 removed outlier: 4.049A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.706A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.674A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN A 409 " --> pdb=" O GLU A 406 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 77 removed outlier: 3.968A pdb=" N THR H 77 " --> pdb=" O SER H 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 126 removed outlier: 3.598A pdb=" N LEU L 125 " --> pdb=" O ASP L 122 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.689A pdb=" N ILE A 402 " --> pdb=" O TYR A 508 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 356 through 358 Processing sheet with id=AA3, first strand: chain 'H' and resid 4 through 6 removed outlier: 3.599A pdb=" N VAL H 5 " --> pdb=" O LYS H 23 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.896A pdb=" N LYS H 12 " --> pdb=" O THR H 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'H' and resid 18 through 19 Processing sheet with id=AA6, first strand: chain 'H' and resid 33 through 38 removed outlier: 6.146A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL H 52 " --> pdb=" O ASN H 56 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASN H 56 " --> pdb=" O VAL H 52 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 93 through 94 Processing sheet with id=AA8, first strand: chain 'H' and resid 120 through 124 removed outlier: 4.262A pdb=" N GLY H 139 " --> pdb=" O LEU H 124 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N SER H 177 " --> pdb=" O ALA H 168 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ALA H 168 " --> pdb=" O SER H 177 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N SER H 179 " --> pdb=" O PHE H 166 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 198 through 200 removed outlier: 3.504A pdb=" N THR H 205 " --> pdb=" O HIS H 200 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 10 through 12 removed outlier: 5.825A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'L' and resid 20 through 24 Processing sheet with id=AB3, first strand: chain 'L' and resid 33 through 37 removed outlier: 4.059A pdb=" N ALA L 34 " --> pdb=" O GLN L 89 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR L 87 " --> pdb=" O TYR L 36 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 117 through 118 removed outlier: 3.538A pdb=" N THR L 178 " --> pdb=" O GLN L 160 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN L 160 " --> pdb=" O THR L 178 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 146 through 147 removed outlier: 3.520A pdb=" N GLU L 195 " --> pdb=" O GLN L 147 " (cutoff:3.500A) 74 hydrogen bonds defined for protein. 171 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.19 Time building geometry restraints manager: 1.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 1544 1.35 - 1.48: 1377 1.48 - 1.60: 2037 1.60 - 1.73: 0 1.73 - 1.85: 26 Bond restraints: 4984 Sorted by residual: bond pdb=" C1 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.46e+00 bond pdb=" C1 MAN B 4 " pdb=" C2 MAN B 4 " ideal model delta sigma weight residual 1.526 1.569 -0.043 2.00e-02 2.50e+03 4.73e+00 bond pdb=" C1 BMA B 3 " pdb=" C2 BMA B 3 " ideal model delta sigma weight residual 1.519 1.560 -0.041 2.00e-02 2.50e+03 4.30e+00 bond pdb=" C1 MAN B 4 " pdb=" O5 MAN B 4 " ideal model delta sigma weight residual 1.399 1.432 -0.033 2.00e-02 2.50e+03 2.72e+00 bond pdb=" C GLN A 498 " pdb=" N PRO A 499 " ideal model delta sigma weight residual 1.334 1.346 -0.013 8.40e-03 1.42e+04 2.34e+00 ... (remaining 4979 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 6440 1.62 - 3.25: 262 3.25 - 4.87: 59 4.87 - 6.49: 15 6.49 - 8.12: 6 Bond angle restraints: 6782 Sorted by residual: angle pdb=" C THR H 191 " pdb=" N GLN H 192 " pdb=" CA GLN H 192 " ideal model delta sigma weight residual 121.54 128.49 -6.95 1.91e+00 2.74e-01 1.33e+01 angle pdb=" CA CYS A 379 " pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " ideal model delta sigma weight residual 114.40 122.52 -8.12 2.30e+00 1.89e-01 1.25e+01 angle pdb=" C PHE A 347 " pdb=" N ALA A 348 " pdb=" CA ALA A 348 " ideal model delta sigma weight residual 121.54 128.07 -6.53 1.91e+00 2.74e-01 1.17e+01 angle pdb=" C SER L 30 " pdb=" N SER L 31 " pdb=" CA SER L 31 " ideal model delta sigma weight residual 121.54 127.13 -5.59 1.91e+00 2.74e-01 8.56e+00 angle pdb=" CA GLY H 55 " pdb=" C GLY H 55 " pdb=" N ASN H 56 " ideal model delta sigma weight residual 117.06 114.03 3.03 1.08e+00 8.57e-01 7.89e+00 ... (remaining 6777 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.98: 2835 22.98 - 45.97: 165 45.97 - 68.95: 14 68.95 - 91.94: 12 91.94 - 114.92: 4 Dihedral angle restraints: 3030 sinusoidal: 1225 harmonic: 1805 Sorted by residual: dihedral pdb=" CB CYS L 134 " pdb=" SG CYS L 134 " pdb=" SG CYS L 194 " pdb=" CB CYS L 194 " ideal model delta sinusoidal sigma weight residual 93.00 179.47 -86.47 1 1.00e+01 1.00e-02 9.01e+01 dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 15.07 77.93 1 1.00e+01 1.00e-02 7.59e+01 dihedral pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " pdb=" SG CYS A 432 " pdb=" CB CYS A 432 " ideal model delta sinusoidal sigma weight residual 93.00 32.88 60.12 1 1.00e+01 1.00e-02 4.82e+01 ... (remaining 3027 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 568 0.051 - 0.101: 154 0.101 - 0.152: 35 0.152 - 0.203: 4 0.203 - 0.254: 2 Chirality restraints: 763 Sorted by residual: chirality pdb=" C5 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C6 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CB ILE L 48 " pdb=" CA ILE L 48 " pdb=" CG1 ILE L 48 " pdb=" CG2 ILE L 48 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA LYS H 201 " pdb=" N LYS H 201 " pdb=" C LYS H 201 " pdb=" CB LYS H 201 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.34e-01 ... (remaining 760 not shown) Planarity restraints: 868 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA L 112 " -0.034 5.00e-02 4.00e+02 5.16e-02 4.26e+00 pdb=" N PRO L 113 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO L 113 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO L 113 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 429 " 0.014 2.00e-02 2.50e+03 1.53e-02 4.12e+00 pdb=" CG PHE A 429 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE A 429 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 429 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE A 429 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A 429 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 429 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 411 " -0.031 5.00e-02 4.00e+02 4.75e-02 3.62e+00 pdb=" N PRO A 412 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 412 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 412 " -0.027 5.00e-02 4.00e+02 ... (remaining 865 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 212 2.70 - 3.25: 5009 3.25 - 3.80: 7178 3.80 - 4.35: 9034 4.35 - 4.90: 14971 Nonbonded interactions: 36404 Sorted by model distance: nonbonded pdb=" OG1 THR H 28 " pdb=" O CYS H 97 " model vdw 2.150 3.040 nonbonded pdb=" OG1 THR L 20 " pdb=" O LEU L 73 " model vdw 2.196 3.040 nonbonded pdb=" O THR A 393 " pdb=" OG1 THR A 523 " model vdw 2.201 3.040 nonbonded pdb=" O ARG L 61 " pdb=" OG SER L 76 " model vdw 2.204 3.040 nonbonded pdb=" NH2 ARG A 357 " pdb=" OH TYR A 396 " model vdw 2.236 3.120 ... (remaining 36399 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.110 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 18.620 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6220 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 : 0.004 0.055 4998 Z= 0.191 Angle : 0.843 11.298 6815 Z= 0.426 Chirality : 0.050 0.254 763 Planarity : 0.005 0.052 867 Dihedral : 14.730 114.921 1851 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 18.13 Ramachandran Plot: Outliers : 0.16 % Allowed : 17.37 % Favored : 82.47 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.08 (0.31), residues: 616 helix: -4.58 (0.49), residues: 20 sheet: -2.30 (0.39), residues: 167 loop : -2.99 (0.28), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP H 47 HIS 0.004 0.001 HIS H 200 PHE 0.036 0.002 PHE A 429 TYR 0.029 0.002 TYR L 49 ARG 0.009 0.001 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00775 ( 1) link_NAG-ASN : angle 7.33545 ( 3) link_ALPHA1-6 : bond 0.00424 ( 1) link_ALPHA1-6 : angle 1.56509 ( 3) link_BETA1-4 : bond 0.00838 ( 2) link_BETA1-4 : angle 2.22433 ( 6) link_ALPHA1-3 : bond 0.00684 ( 1) link_ALPHA1-3 : angle 1.08998 ( 3) hydrogen bonds : bond 0.28352 ( 68) hydrogen bonds : angle 12.41165 ( 171) SS BOND : bond 0.00691 ( 9) SS BOND : angle 1.84933 ( 18) covalent geometry : bond 0.00407 ( 4984) covalent geometry : angle 0.82130 ( 6782) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 ILE cc_start: 0.8718 (mp) cc_final: 0.8491 (mm) REVERT: H 72 ASP cc_start: 0.7392 (t0) cc_final: 0.6045 (t0) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.2486 time to fit residues: 27.5474 Evaluate side-chains 69 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 0.2980 chunk 31 optimal weight: 3.9990 chunk 24 optimal weight: 0.3980 chunk 47 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 138 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.093917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.085507 restraints weight = 22649.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.087323 restraints weight = 14133.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.088559 restraints weight = 9720.246| |-----------------------------------------------------------------------------| r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3952 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3952 r_free = 0.3952 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3951 r_free = 0.3951 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3951 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6599 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 4998 Z= 0.171 Angle : 0.801 11.514 6815 Z= 0.402 Chirality : 0.049 0.180 763 Planarity : 0.006 0.050 867 Dihedral : 11.324 91.494 777 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.16 % Allowed : 16.23 % Favored : 83.60 % Rotamer: Outliers : 1.31 % Allowed : 12.15 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.25 (0.30), residues: 616 helix: -4.10 (0.49), residues: 26 sheet: -2.32 (0.39), residues: 168 loop : -3.16 (0.27), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP L 35 HIS 0.005 0.001 HIS L 189 PHE 0.024 0.002 PHE H 27 TYR 0.014 0.002 TYR H 96 ARG 0.008 0.001 ARG H 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00674 ( 1) link_NAG-ASN : angle 7.78562 ( 3) link_ALPHA1-6 : bond 0.00823 ( 1) link_ALPHA1-6 : angle 1.50407 ( 3) link_BETA1-4 : bond 0.00804 ( 2) link_BETA1-4 : angle 2.66255 ( 6) link_ALPHA1-3 : bond 0.01498 ( 1) link_ALPHA1-3 : angle 1.83905 ( 3) hydrogen bonds : bond 0.05241 ( 68) hydrogen bonds : angle 8.79011 ( 171) SS BOND : bond 0.00642 ( 9) SS BOND : angle 1.66165 ( 18) covalent geometry : bond 0.00380 ( 4984) covalent geometry : angle 0.77553 ( 6782) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 0.634 Fit side-chains revert: symmetry clash REVERT: A 402 ILE cc_start: 0.8831 (mp) cc_final: 0.8590 (mm) REVERT: H 38 ARG cc_start: 0.8108 (tmm-80) cc_final: 0.7812 (tmm-80) REVERT: H 72 ASP cc_start: 0.8321 (t0) cc_final: 0.7666 (t0) outliers start: 7 outliers final: 5 residues processed: 80 average time/residue: 0.2434 time to fit residues: 24.6144 Evaluate side-chains 76 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 180 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 6 optimal weight: 0.0270 chunk 25 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.096194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.086824 restraints weight = 22032.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.088959 restraints weight = 12908.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.090398 restraints weight = 8497.796| |-----------------------------------------------------------------------------| r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3955 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3955 r_free = 0.3955 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3955 r_free = 0.3955 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3955 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6484 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 4998 Z= 0.151 Angle : 0.782 12.015 6815 Z= 0.388 Chirality : 0.048 0.164 763 Planarity : 0.005 0.049 867 Dihedral : 10.451 80.948 777 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.16 % Allowed : 16.23 % Favored : 83.60 % Rotamer: Outliers : 0.93 % Allowed : 17.76 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.30 (0.30), residues: 616 helix: -3.98 (0.54), residues: 26 sheet: -2.28 (0.39), residues: 165 loop : -3.24 (0.27), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 47 HIS 0.003 0.001 HIS L 189 PHE 0.027 0.002 PHE H 27 TYR 0.012 0.001 TYR A 453 ARG 0.007 0.001 ARG H 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00490 ( 1) link_NAG-ASN : angle 8.17923 ( 3) link_ALPHA1-6 : bond 0.00810 ( 1) link_ALPHA1-6 : angle 1.43677 ( 3) link_BETA1-4 : bond 0.00874 ( 2) link_BETA1-4 : angle 2.59593 ( 6) link_ALPHA1-3 : bond 0.01304 ( 1) link_ALPHA1-3 : angle 1.46517 ( 3) hydrogen bonds : bond 0.04204 ( 68) hydrogen bonds : angle 8.35482 ( 171) SS BOND : bond 0.00618 ( 9) SS BOND : angle 1.48422 ( 18) covalent geometry : bond 0.00334 ( 4984) covalent geometry : angle 0.75612 ( 6782) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 80 time to evaluate : 0.639 Fit side-chains revert: symmetry clash REVERT: A 402 ILE cc_start: 0.8851 (mp) cc_final: 0.8576 (mm) REVERT: H 72 ASP cc_start: 0.8217 (t0) cc_final: 0.7878 (t0) outliers start: 5 outliers final: 5 residues processed: 82 average time/residue: 0.2642 time to fit residues: 26.9990 Evaluate side-chains 75 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 180 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 24 optimal weight: 3.9990 chunk 17 optimal weight: 0.4980 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 2 optimal weight: 0.0670 chunk 22 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 59 optimal weight: 0.4980 chunk 0 optimal weight: 2.9990 overall best weight: 0.5520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.094445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.085125 restraints weight = 22290.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.087279 restraints weight = 13133.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.088715 restraints weight = 8616.749| |-----------------------------------------------------------------------------| r_work (final): 0.3936 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3935 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3935 r_free = 0.3935 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3935 r_free = 0.3935 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3935 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6578 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4998 Z= 0.139 Angle : 0.752 12.134 6815 Z= 0.375 Chirality : 0.047 0.167 763 Planarity : 0.005 0.048 867 Dihedral : 9.119 65.177 777 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.16 % Allowed : 16.07 % Favored : 83.77 % Rotamer: Outliers : 2.06 % Allowed : 18.50 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.26 (0.30), residues: 616 helix: -3.91 (0.58), residues: 27 sheet: -2.24 (0.40), residues: 160 loop : -3.22 (0.26), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP H 47 HIS 0.003 0.001 HIS L 198 PHE 0.029 0.002 PHE H 27 TYR 0.018 0.001 TYR L 140 ARG 0.006 0.001 ARG H 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00589 ( 1) link_NAG-ASN : angle 8.19353 ( 3) link_ALPHA1-6 : bond 0.00837 ( 1) link_ALPHA1-6 : angle 1.52974 ( 3) link_BETA1-4 : bond 0.00873 ( 2) link_BETA1-4 : angle 2.33339 ( 6) link_ALPHA1-3 : bond 0.01337 ( 1) link_ALPHA1-3 : angle 1.59122 ( 3) hydrogen bonds : bond 0.03705 ( 68) hydrogen bonds : angle 7.73182 ( 171) SS BOND : bond 0.00505 ( 9) SS BOND : angle 1.40260 ( 18) covalent geometry : bond 0.00313 ( 4984) covalent geometry : angle 0.72535 ( 6782) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 1.545 Fit side-chains revert: symmetry clash REVERT: A 402 ILE cc_start: 0.8890 (mp) cc_final: 0.8632 (mm) REVERT: H 72 ASP cc_start: 0.8359 (t0) cc_final: 0.7864 (t0) REVERT: H 144 ASP cc_start: 0.8433 (OUTLIER) cc_final: 0.8001 (t0) REVERT: L 160 GLN cc_start: 0.7590 (mp10) cc_final: 0.6849 (mp10) outliers start: 11 outliers final: 7 residues processed: 88 average time/residue: 0.2763 time to fit residues: 30.9574 Evaluate side-chains 83 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain H residue 144 ASP Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 180 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 45 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 2 optimal weight: 0.0060 chunk 50 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 0.1980 chunk 27 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.094703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.085403 restraints weight = 22436.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.087541 restraints weight = 13225.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.088979 restraints weight = 8688.787| |-----------------------------------------------------------------------------| r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3963 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3963 r_free = 0.3963 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3963 r_free = 0.3963 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3963 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6456 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4998 Z= 0.137 Angle : 0.758 12.044 6815 Z= 0.379 Chirality : 0.049 0.282 763 Planarity : 0.005 0.049 867 Dihedral : 8.008 59.911 777 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.16 % Allowed : 15.75 % Favored : 84.09 % Rotamer: Outliers : 2.80 % Allowed : 19.44 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.27 (0.30), residues: 616 helix: -3.79 (0.60), residues: 27 sheet: -2.34 (0.39), residues: 166 loop : -3.19 (0.26), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.003 0.001 HIS L 198 PHE 0.031 0.002 PHE H 27 TYR 0.037 0.002 TYR L 49 ARG 0.006 0.001 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00626 ( 1) link_NAG-ASN : angle 8.15884 ( 3) link_ALPHA1-6 : bond 0.00912 ( 1) link_ALPHA1-6 : angle 1.81592 ( 3) link_BETA1-4 : bond 0.00878 ( 2) link_BETA1-4 : angle 2.01048 ( 6) link_ALPHA1-3 : bond 0.01217 ( 1) link_ALPHA1-3 : angle 1.68761 ( 3) hydrogen bonds : bond 0.03457 ( 68) hydrogen bonds : angle 7.34235 ( 171) SS BOND : bond 0.00440 ( 9) SS BOND : angle 0.96000 ( 18) covalent geometry : bond 0.00306 ( 4984) covalent geometry : angle 0.73415 ( 6782) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.568 Fit side-chains revert: symmetry clash REVERT: A 402 ILE cc_start: 0.8866 (mp) cc_final: 0.8597 (mm) REVERT: H 72 ASP cc_start: 0.8169 (t0) cc_final: 0.7902 (t0) REVERT: H 100 PHE cc_start: 0.7189 (OUTLIER) cc_final: 0.6939 (t80) REVERT: H 117 LYS cc_start: 0.7300 (pptt) cc_final: 0.6103 (pptt) REVERT: H 144 ASP cc_start: 0.8420 (OUTLIER) cc_final: 0.7378 (t0) outliers start: 15 outliers final: 9 residues processed: 90 average time/residue: 0.1819 time to fit residues: 20.7590 Evaluate side-chains 84 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain H residue 140 CYS Chi-restraints excluded: chain H residue 144 ASP Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 181 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 15 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.091512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.083235 restraints weight = 22288.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.085195 restraints weight = 13116.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.086482 restraints weight = 8580.031| |-----------------------------------------------------------------------------| r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3905 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3905 r_free = 0.3905 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3905 r_free = 0.3905 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3905 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6635 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.111 4998 Z= 0.239 Angle : 0.846 12.215 6815 Z= 0.431 Chirality : 0.050 0.206 763 Planarity : 0.006 0.057 867 Dihedral : 7.489 52.636 777 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 17.20 Ramachandran Plot: Outliers : 0.16 % Allowed : 18.99 % Favored : 80.84 % Rotamer: Outliers : 3.93 % Allowed : 20.00 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.43 (0.30), residues: 616 helix: -3.45 (0.66), residues: 26 sheet: -2.41 (0.38), residues: 165 loop : -3.37 (0.26), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP H 47 HIS 0.003 0.001 HIS L 198 PHE 0.033 0.003 PHE H 27 TYR 0.025 0.002 TYR L 140 ARG 0.010 0.001 ARG H 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00432 ( 1) link_NAG-ASN : angle 8.59417 ( 3) link_ALPHA1-6 : bond 0.00995 ( 1) link_ALPHA1-6 : angle 2.06712 ( 3) link_BETA1-4 : bond 0.00976 ( 2) link_BETA1-4 : angle 1.87876 ( 6) link_ALPHA1-3 : bond 0.01261 ( 1) link_ALPHA1-3 : angle 2.41162 ( 3) hydrogen bonds : bond 0.04182 ( 68) hydrogen bonds : angle 7.66973 ( 171) SS BOND : bond 0.00626 ( 9) SS BOND : angle 1.60804 ( 18) covalent geometry : bond 0.00534 ( 4984) covalent geometry : angle 0.81941 ( 6782) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 75 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 402 ILE cc_start: 0.8960 (mp) cc_final: 0.8662 (mm) REVERT: H 72 ASP cc_start: 0.8207 (t0) cc_final: 0.7793 (t0) REVERT: H 144 ASP cc_start: 0.8464 (OUTLIER) cc_final: 0.7997 (t0) REVERT: L 110 VAL cc_start: 0.5482 (OUTLIER) cc_final: 0.5178 (p) outliers start: 21 outliers final: 9 residues processed: 91 average time/residue: 0.2145 time to fit residues: 24.8790 Evaluate side-chains 81 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain H residue 140 CYS Chi-restraints excluded: chain H residue 144 ASP Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 181 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 46 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 14 optimal weight: 0.0170 chunk 9 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 34 optimal weight: 0.0670 chunk 37 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 overall best weight: 0.5556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.092982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.084668 restraints weight = 22814.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.086534 restraints weight = 14121.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.087809 restraints weight = 9621.121| |-----------------------------------------------------------------------------| r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3949 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3949 r_free = 0.3949 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3949 r_free = 0.3949 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3949 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6499 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4998 Z= 0.144 Angle : 0.796 12.214 6815 Z= 0.398 Chirality : 0.048 0.159 763 Planarity : 0.005 0.051 867 Dihedral : 7.066 57.896 777 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.16 % Allowed : 14.45 % Favored : 85.39 % Rotamer: Outliers : 2.62 % Allowed : 21.50 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.32 (0.30), residues: 616 helix: -3.39 (0.69), residues: 27 sheet: -2.40 (0.40), residues: 160 loop : -3.24 (0.26), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP H 47 HIS 0.003 0.001 HIS L 189 PHE 0.037 0.002 PHE H 27 TYR 0.019 0.001 TYR L 140 ARG 0.008 0.001 ARG H 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00615 ( 1) link_NAG-ASN : angle 8.32280 ( 3) link_ALPHA1-6 : bond 0.00951 ( 1) link_ALPHA1-6 : angle 2.24547 ( 3) link_BETA1-4 : bond 0.00981 ( 2) link_BETA1-4 : angle 1.66872 ( 6) link_ALPHA1-3 : bond 0.01436 ( 1) link_ALPHA1-3 : angle 1.86672 ( 3) hydrogen bonds : bond 0.03507 ( 68) hydrogen bonds : angle 7.33652 ( 171) SS BOND : bond 0.00451 ( 9) SS BOND : angle 1.35335 ( 18) covalent geometry : bond 0.00328 ( 4984) covalent geometry : angle 0.77183 ( 6782) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 402 ILE cc_start: 0.8894 (mp) cc_final: 0.8616 (mm) REVERT: H 72 ASP cc_start: 0.8173 (t0) cc_final: 0.7799 (t0) REVERT: H 117 LYS cc_start: 0.7428 (pptt) cc_final: 0.6156 (pptt) REVERT: H 144 ASP cc_start: 0.8460 (OUTLIER) cc_final: 0.7435 (t0) REVERT: L 110 VAL cc_start: 0.5568 (OUTLIER) cc_final: 0.5314 (p) outliers start: 14 outliers final: 9 residues processed: 85 average time/residue: 0.2302 time to fit residues: 25.6918 Evaluate side-chains 82 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain H residue 140 CYS Chi-restraints excluded: chain H residue 144 ASP Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain L residue 189 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 4 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 52 optimal weight: 0.0980 chunk 27 optimal weight: 0.0070 chunk 49 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 15 optimal weight: 0.2980 chunk 8 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 overall best weight: 0.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 58 ASN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.093856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.085620 restraints weight = 22856.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.087454 restraints weight = 14088.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.088698 restraints weight = 9573.004| |-----------------------------------------------------------------------------| r_work (final): 0.3971 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3971 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3971 r_free = 0.3971 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3971 r_free = 0.3971 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3971 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6455 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4998 Z= 0.133 Angle : 0.768 11.631 6815 Z= 0.384 Chirality : 0.047 0.153 763 Planarity : 0.005 0.046 867 Dihedral : 6.565 58.292 777 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.16 % Allowed : 16.56 % Favored : 83.28 % Rotamer: Outliers : 3.18 % Allowed : 22.06 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.18 (0.30), residues: 616 helix: -3.51 (0.66), residues: 27 sheet: -2.39 (0.40), residues: 164 loop : -3.09 (0.27), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 47 HIS 0.002 0.001 HIS L 198 PHE 0.036 0.002 PHE H 27 TYR 0.017 0.001 TYR L 140 ARG 0.007 0.001 ARG H 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00620 ( 1) link_NAG-ASN : angle 7.93045 ( 3) link_ALPHA1-6 : bond 0.00728 ( 1) link_ALPHA1-6 : angle 2.19138 ( 3) link_BETA1-4 : bond 0.00830 ( 2) link_BETA1-4 : angle 1.42254 ( 6) link_ALPHA1-3 : bond 0.01360 ( 1) link_ALPHA1-3 : angle 1.87712 ( 3) hydrogen bonds : bond 0.03333 ( 68) hydrogen bonds : angle 7.00129 ( 171) SS BOND : bond 0.00372 ( 9) SS BOND : angle 1.33387 ( 18) covalent geometry : bond 0.00305 ( 4984) covalent geometry : angle 0.74526 ( 6782) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 402 ILE cc_start: 0.8882 (mp) cc_final: 0.8607 (mm) REVERT: H 72 ASP cc_start: 0.8097 (t0) cc_final: 0.7754 (t0) REVERT: H 117 LYS cc_start: 0.7238 (pptt) cc_final: 0.6047 (pptt) REVERT: H 144 ASP cc_start: 0.8397 (OUTLIER) cc_final: 0.7433 (t0) REVERT: L 110 VAL cc_start: 0.5516 (OUTLIER) cc_final: 0.5275 (p) REVERT: L 175 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7759 (mt) outliers start: 17 outliers final: 9 residues processed: 85 average time/residue: 0.2322 time to fit residues: 25.8128 Evaluate side-chains 86 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain H residue 140 CYS Chi-restraints excluded: chain H residue 144 ASP Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain L residue 189 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 4 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 26 optimal weight: 0.0870 chunk 32 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 36 optimal weight: 0.0170 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.093848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.085646 restraints weight = 22895.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.087475 restraints weight = 14057.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.088711 restraints weight = 9564.892| |-----------------------------------------------------------------------------| r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3969 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3969 r_free = 0.3969 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3969 r_free = 0.3969 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3969 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6454 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4998 Z= 0.137 Angle : 0.775 11.433 6815 Z= 0.385 Chirality : 0.048 0.313 763 Planarity : 0.005 0.051 867 Dihedral : 6.491 58.396 777 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.16 % Allowed : 15.91 % Favored : 83.93 % Rotamer: Outliers : 2.24 % Allowed : 22.99 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.16 (0.31), residues: 616 helix: -3.46 (0.67), residues: 27 sheet: -2.36 (0.39), residues: 173 loop : -3.09 (0.27), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP H 47 HIS 0.003 0.001 HIS L 198 PHE 0.034 0.002 PHE H 27 TYR 0.019 0.001 TYR L 140 ARG 0.006 0.001 ARG H 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00622 ( 1) link_NAG-ASN : angle 7.74513 ( 3) link_ALPHA1-6 : bond 0.00883 ( 1) link_ALPHA1-6 : angle 2.15951 ( 3) link_BETA1-4 : bond 0.00787 ( 2) link_BETA1-4 : angle 1.38875 ( 6) link_ALPHA1-3 : bond 0.01213 ( 1) link_ALPHA1-3 : angle 1.79130 ( 3) hydrogen bonds : bond 0.03386 ( 68) hydrogen bonds : angle 6.88408 ( 171) SS BOND : bond 0.00447 ( 9) SS BOND : angle 1.25732 ( 18) covalent geometry : bond 0.00315 ( 4984) covalent geometry : angle 0.75338 ( 6782) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 402 ILE cc_start: 0.8877 (mp) cc_final: 0.8607 (mm) REVERT: H 72 ASP cc_start: 0.8134 (t0) cc_final: 0.7766 (t0) REVERT: H 117 LYS cc_start: 0.7239 (pptt) cc_final: 0.6022 (pptt) REVERT: H 144 ASP cc_start: 0.8419 (OUTLIER) cc_final: 0.7460 (t0) REVERT: L 110 VAL cc_start: 0.5578 (OUTLIER) cc_final: 0.5338 (p) REVERT: L 117 ILE cc_start: 0.7135 (tt) cc_final: 0.6687 (tp) outliers start: 12 outliers final: 9 residues processed: 83 average time/residue: 0.2493 time to fit residues: 26.5748 Evaluate side-chains 84 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain H residue 140 CYS Chi-restraints excluded: chain H residue 144 ASP Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain L residue 189 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 24 optimal weight: 4.9990 chunk 58 optimal weight: 0.4980 chunk 60 optimal weight: 5.9990 chunk 16 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 0.3980 chunk 27 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 43 optimal weight: 0.3980 chunk 51 optimal weight: 3.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.093855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.085605 restraints weight = 22886.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.087433 restraints weight = 14103.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.088682 restraints weight = 9621.657| |-----------------------------------------------------------------------------| r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3968 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3968 r_free = 0.3968 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3968 r_free = 0.3968 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3968 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6457 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4998 Z= 0.139 Angle : 0.789 11.247 6815 Z= 0.391 Chirality : 0.048 0.221 763 Planarity : 0.005 0.047 867 Dihedral : 6.398 58.454 777 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.16 % Allowed : 16.07 % Favored : 83.77 % Rotamer: Outliers : 2.24 % Allowed : 24.30 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.10 (0.31), residues: 616 helix: -3.47 (0.67), residues: 27 sheet: -2.33 (0.39), residues: 173 loop : -3.03 (0.28), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP H 47 HIS 0.002 0.001 HIS L 198 PHE 0.034 0.002 PHE H 27 TYR 0.019 0.001 TYR L 140 ARG 0.006 0.001 ARG H 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00613 ( 1) link_NAG-ASN : angle 7.57033 ( 3) link_ALPHA1-6 : bond 0.00902 ( 1) link_ALPHA1-6 : angle 2.12275 ( 3) link_BETA1-4 : bond 0.00773 ( 2) link_BETA1-4 : angle 1.37167 ( 6) link_ALPHA1-3 : bond 0.01120 ( 1) link_ALPHA1-3 : angle 1.73411 ( 3) hydrogen bonds : bond 0.03300 ( 68) hydrogen bonds : angle 6.77185 ( 171) SS BOND : bond 0.00392 ( 9) SS BOND : angle 1.20470 ( 18) covalent geometry : bond 0.00323 ( 4984) covalent geometry : angle 0.76893 ( 6782) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 402 ILE cc_start: 0.8872 (mp) cc_final: 0.8594 (mm) REVERT: H 72 ASP cc_start: 0.8161 (t0) cc_final: 0.7827 (t0) REVERT: H 117 LYS cc_start: 0.7224 (pptt) cc_final: 0.5989 (pptt) REVERT: H 144 ASP cc_start: 0.8391 (OUTLIER) cc_final: 0.7446 (t0) REVERT: L 110 VAL cc_start: 0.5581 (OUTLIER) cc_final: 0.5338 (p) REVERT: L 117 ILE cc_start: 0.7044 (tt) cc_final: 0.6603 (tp) outliers start: 12 outliers final: 9 residues processed: 86 average time/residue: 0.3429 time to fit residues: 39.4794 Evaluate side-chains 84 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain H residue 140 CYS Chi-restraints excluded: chain H residue 144 ASP Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain L residue 189 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 49 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 48 optimal weight: 0.0980 chunk 26 optimal weight: 0.0870 chunk 36 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 18 optimal weight: 0.4980 chunk 12 optimal weight: 0.8980 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.094335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.086114 restraints weight = 22971.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.087928 restraints weight = 14148.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.089167 restraints weight = 9653.392| |-----------------------------------------------------------------------------| r_work (final): 0.3978 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3978 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3978 r_free = 0.3978 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3978 r_free = 0.3978 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3978 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6431 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4998 Z= 0.133 Angle : 0.779 10.913 6815 Z= 0.387 Chirality : 0.047 0.168 763 Planarity : 0.005 0.052 867 Dihedral : 6.266 59.389 777 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.16 % Allowed : 14.45 % Favored : 85.39 % Rotamer: Outliers : 2.24 % Allowed : 23.93 % Favored : 73.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.08 (0.31), residues: 616 helix: -3.53 (0.66), residues: 27 sheet: -2.34 (0.39), residues: 173 loop : -3.00 (0.28), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP H 47 HIS 0.002 0.001 HIS L 189 PHE 0.033 0.002 PHE H 27 TYR 0.017 0.001 TYR L 140 ARG 0.006 0.001 ARG H 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00609 ( 1) link_NAG-ASN : angle 7.27882 ( 3) link_ALPHA1-6 : bond 0.00849 ( 1) link_ALPHA1-6 : angle 2.07266 ( 3) link_BETA1-4 : bond 0.00844 ( 2) link_BETA1-4 : angle 1.35848 ( 6) link_ALPHA1-3 : bond 0.00979 ( 1) link_ALPHA1-3 : angle 1.54230 ( 3) hydrogen bonds : bond 0.03221 ( 68) hydrogen bonds : angle 6.64689 ( 171) SS BOND : bond 0.00370 ( 9) SS BOND : angle 1.18467 ( 18) covalent geometry : bond 0.00311 ( 4984) covalent geometry : angle 0.76068 ( 6782) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4755.44 seconds wall clock time: 88 minutes 56.69 seconds (5336.69 seconds total)