Starting phenix.real_space_refine on Fri Aug 2 15:16:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vif_43260/08_2024/8vif_43260.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vif_43260/08_2024/8vif_43260.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vif_43260/08_2024/8vif_43260.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vif_43260/08_2024/8vif_43260.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vif_43260/08_2024/8vif_43260.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vif_43260/08_2024/8vif_43260.cif" } resolution = 3.1 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= 0.027 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 2109 2.51 5 N 557 2.21 5 O 645 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H GLU 6": "OE1" <-> "OE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H GLU 56": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 3326 Number of models: 1 Model: "" Number of chains: 4 Chain: "H" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 991 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "L" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 825 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 7, 'TRANS': 105} Chain: "R" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1496 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 10, 'TRANS': 175} Chain breaks: 1 Chain: "R" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.38, per 1000 atoms: 1.32 Number of scatterers: 3326 At special positions: 0 Unit cell: (77.08, 81.78, 67.68, 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 645 8.00 N 557 7.00 C 2109 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS R 336 " - pdb=" SG CYS R 361 " distance=2.04 Simple disulfide: pdb=" SG CYS R 379 " - pdb=" SG CYS R 432 " distance=2.03 Simple disulfide: pdb=" SG CYS R 391 " - pdb=" SG CYS R 525 " distance=2.03 Simple disulfide: pdb=" SG CYS R 480 " - pdb=" SG CYS R 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG R1301 " - " ASN R 343 " Time building additional restraints: 1.12 Conformation dependent library (CDL) restraints added in 535.1 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: 786 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 10 sheets defined 11.9% alpha, 35.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.547A pdb=" N THR H 87 " --> pdb=" O PRO H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 100A No H-bonds generated for 'chain 'H' and resid 99 through 100A' Processing helix chain 'L' and resid 27A through 30 Processing helix chain 'R' and resid 338 through 343 Processing helix chain 'R' and resid 349 through 353 removed outlier: 3.598A pdb=" N TRP R 353 " --> pdb=" O VAL R 350 " (cutoff:3.500A) Processing helix chain 'R' and resid 364 through 372 removed outlier: 3.524A pdb=" N LEU R 368 " --> pdb=" O ASP R 364 " (cutoff:3.500A) Processing helix chain 'R' and resid 383 through 387 removed outlier: 3.651A pdb=" N LEU R 387 " --> pdb=" O PRO R 384 " (cutoff:3.500A) Processing helix chain 'R' and resid 406 through 410 Processing helix chain 'R' and resid 416 through 422 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 7.023A pdb=" N VAL H 35A" --> pdb=" O ASP H 50 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ASP H 50 " --> pdb=" O VAL H 35A" (cutoff:3.500A) removed outlier: 6.608A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 4.063A pdb=" N ASN H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ALA H 96 " --> pdb=" O PHE H 100K" (cutoff:3.500A) removed outlier: 4.934A pdb=" N PHE H 100K" --> pdb=" O ALA H 96 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 100C through 100E Processing sheet with id=AA5, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.449A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 9 through 13 Processing sheet with id=AA7, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AA8, first strand: chain 'R' and resid 361 through 362 removed outlier: 6.714A pdb=" N CYS R 361 " --> pdb=" O CYS R 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'R' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'R' and resid 473 through 474 124 hydrogen bonds defined for protein. 279 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.87 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1060 1.34 - 1.46: 860 1.46 - 1.58: 1470 1.58 - 1.69: 0 1.69 - 1.81: 18 Bond restraints: 3408 Sorted by residual: bond pdb=" C GLN H 39 " pdb=" N PRO H 40 " ideal model delta sigma weight residual 1.335 1.363 -0.029 1.15e-02 7.56e+03 6.15e+00 bond pdb=" N LYS H 43 " pdb=" CA LYS H 43 " ideal model delta sigma weight residual 1.456 1.485 -0.030 1.44e-02 4.82e+03 4.25e+00 bond pdb=" N GLY H 42 " pdb=" CA GLY H 42 " ideal model delta sigma weight residual 1.450 1.475 -0.025 1.38e-02 5.25e+03 3.22e+00 bond pdb=" C1 NAG R1301 " pdb=" O5 NAG R1301 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.90e+00 bond pdb=" CA LEU L 78 " pdb=" C LEU L 78 " ideal model delta sigma weight residual 1.529 1.517 0.012 1.04e-02 9.25e+03 1.31e+00 ... (remaining 3403 not shown) Histogram of bond angle deviations from ideal: 100.79 - 107.43: 118 107.43 - 114.08: 1852 114.08 - 120.73: 1334 120.73 - 127.37: 1297 127.37 - 134.02: 34 Bond angle restraints: 4635 Sorted by residual: angle pdb=" N PRO H 40 " pdb=" CA PRO H 40 " pdb=" CB PRO H 40 " ideal model delta sigma weight residual 103.22 105.11 -1.89 5.20e-01 3.70e+00 1.32e+01 angle pdb=" C ASN L 51 " pdb=" N ASN L 52 " pdb=" CA ASN L 52 " ideal model delta sigma weight residual 122.08 126.62 -4.54 1.47e+00 4.63e-01 9.52e+00 angle pdb=" CA GLY R 502 " pdb=" C GLY R 502 " pdb=" O GLY R 502 " ideal model delta sigma weight residual 122.29 120.15 2.14 8.10e-01 1.52e+00 6.96e+00 angle pdb=" CA LYS H 43 " pdb=" C LYS H 43 " pdb=" O LYS H 43 " ideal model delta sigma weight residual 121.49 118.46 3.03 1.16e+00 7.43e-01 6.80e+00 angle pdb=" CA GLY H 100C" pdb=" C GLY H 100C" pdb=" N TYR H 100D" ideal model delta sigma weight residual 114.85 117.19 -2.34 9.50e-01 1.11e+00 6.08e+00 ... (remaining 4630 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.09: 1797 16.09 - 32.18: 173 32.18 - 48.26: 43 48.26 - 64.35: 12 64.35 - 80.44: 3 Dihedral angle restraints: 2028 sinusoidal: 794 harmonic: 1234 Sorted by residual: dihedral pdb=" CB CYS R 480 " pdb=" SG CYS R 480 " pdb=" SG CYS R 488 " pdb=" CB CYS R 488 " ideal model delta sinusoidal sigma weight residual 93.00 162.90 -69.90 1 1.00e+01 1.00e-02 6.30e+01 dihedral pdb=" CB CYS R 336 " pdb=" SG CYS R 336 " pdb=" SG CYS R 361 " pdb=" CB CYS R 361 " ideal model delta sinusoidal sigma weight residual -86.00 -45.89 -40.11 1 1.00e+01 1.00e-02 2.26e+01 dihedral pdb=" CA ASN H 97 " pdb=" C ASN H 97 " pdb=" N TYR H 98 " pdb=" CA TYR H 98 " ideal model delta harmonic sigma weight residual 180.00 156.95 23.05 0 5.00e+00 4.00e-02 2.12e+01 ... (remaining 2025 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 307 0.033 - 0.066: 139 0.066 - 0.100: 37 0.100 - 0.133: 25 0.133 - 0.166: 3 Chirality restraints: 511 Sorted by residual: chirality pdb=" CA ILE L 48 " pdb=" N ILE L 48 " pdb=" C ILE L 48 " pdb=" CB ILE L 48 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.90e-01 chirality pdb=" CA PRO H 41 " pdb=" N PRO H 41 " pdb=" C PRO H 41 " pdb=" CB PRO H 41 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.45e-01 chirality pdb=" CA ASP H 99 " pdb=" N ASP H 99 " pdb=" C ASP H 99 " pdb=" CB ASP H 99 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.59e-01 ... (remaining 508 not shown) Planarity restraints: 597 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA L 14 " -0.063 5.00e-02 4.00e+02 9.53e-02 1.45e+01 pdb=" N PRO L 15 " 0.165 5.00e-02 4.00e+02 pdb=" CA PRO L 15 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO L 15 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO L 7 " -0.050 5.00e-02 4.00e+02 7.56e-02 9.15e+00 pdb=" N PRO L 8 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO L 8 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO L 8 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR R 369 " 0.007 2.00e-02 2.50e+03 8.07e-03 1.30e+00 pdb=" CG TYR R 369 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR R 369 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR R 369 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR R 369 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR R 369 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR R 369 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR R 369 " 0.000 2.00e-02 2.50e+03 ... (remaining 594 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 191 2.73 - 3.27: 3152 3.27 - 3.81: 5374 3.81 - 4.36: 6810 4.36 - 4.90: 11893 Nonbonded interactions: 27420 Sorted by model distance: nonbonded pdb=" O ASN H 31 " pdb=" OG SER H 53 " model vdw 2.184 3.040 nonbonded pdb=" OD1 ASP H 55 " pdb=" NH1 ARG H 71 " model vdw 2.205 3.120 nonbonded pdb=" O ARG H 100F" pdb=" NH2 ARG L 96 " model vdw 2.364 3.120 nonbonded pdb=" NH2 ARG H 66 " pdb=" OD2 ASP H 86 " model vdw 2.368 3.120 nonbonded pdb=" OD1 ASN L 27B" pdb=" N ILE L 27C" model vdw 2.381 3.120 ... (remaining 27415 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.040 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 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 0.037 3408 Z= 0.249 Angle : 0.613 5.356 4635 Z= 0.360 Chirality : 0.045 0.166 511 Planarity : 0.006 0.095 596 Dihedral : 13.827 80.441 1224 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.00 % Allowed : 14.40 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.05 (0.40), residues: 419 helix: -2.67 (1.00), residues: 19 sheet: 0.80 (0.45), residues: 146 loop : -0.16 (0.37), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.001 0.001 HIS R 505 PHE 0.010 0.001 PHE L 91 TYR 0.020 0.002 TYR R 369 ARG 0.002 0.000 ARG R 346 *********************** 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 49 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.388 Fit side-chains REVERT: H 41 PRO cc_start: 0.8750 (Cg_endo) cc_final: 0.8532 (Cg_exo) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1690 time to fit residues: 10.1814 Evaluate side-chains 49 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 17 optimal weight: 0.1980 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 12 optimal weight: 0.0670 chunk 19 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 0.0670 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 100JGLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.0847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3408 Z= 0.217 Angle : 0.538 5.190 4635 Z= 0.288 Chirality : 0.045 0.151 511 Planarity : 0.005 0.065 596 Dihedral : 5.493 53.448 489 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.63 % Allowed : 14.67 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.06 (0.40), residues: 419 helix: -2.97 (0.91), residues: 19 sheet: 0.57 (0.44), residues: 154 loop : 0.03 (0.38), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 47 HIS 0.001 0.001 HIS R 505 PHE 0.009 0.001 PHE L 62 TYR 0.018 0.001 TYR L 49 ARG 0.003 0.000 ARG R 403 *********************** 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 56 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 50 time to evaluate : 0.387 Fit side-chains REVERT: H 43 LYS cc_start: 0.8652 (mmtp) cc_final: 0.8268 (mttm) REVERT: H 56 GLU cc_start: 0.8301 (mt-10) cc_final: 0.8042 (mm-30) REVERT: R 501 TYR cc_start: 0.7362 (m-10) cc_final: 0.7093 (m-10) outliers start: 6 outliers final: 5 residues processed: 54 average time/residue: 0.1760 time to fit residues: 11.6058 Evaluate side-chains 53 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 48 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 415 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 100JGLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 3408 Z= 0.322 Angle : 0.586 6.239 4635 Z= 0.312 Chirality : 0.047 0.158 511 Planarity : 0.005 0.052 596 Dihedral : 5.783 52.719 489 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.72 % Allowed : 15.76 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.24 (0.39), residues: 419 helix: -3.24 (0.85), residues: 19 sheet: 0.37 (0.44), residues: 149 loop : -0.16 (0.36), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 47 HIS 0.002 0.001 HIS R 505 PHE 0.012 0.001 PHE L 91 TYR 0.025 0.002 TYR L 49 ARG 0.003 0.000 ARG R 403 *********************** 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 58 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 48 time to evaluate : 0.385 Fit side-chains REVERT: H 43 LYS cc_start: 0.8698 (mmtp) cc_final: 0.8375 (mttm) REVERT: R 501 TYR cc_start: 0.7491 (m-10) cc_final: 0.7221 (m-10) outliers start: 10 outliers final: 7 residues processed: 55 average time/residue: 0.1497 time to fit residues: 10.2918 Evaluate side-chains 55 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 48 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 50 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 415 THR Chi-restraints excluded: chain R residue 470 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 4 optimal weight: 0.0170 chunk 17 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.7420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 100JGLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 3408 Z= 0.325 Angle : 0.585 6.214 4635 Z= 0.310 Chirality : 0.047 0.158 511 Planarity : 0.005 0.046 596 Dihedral : 5.850 53.055 489 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.99 % Allowed : 16.03 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.55 (0.39), residues: 419 helix: -3.86 (0.68), residues: 25 sheet: 0.31 (0.44), residues: 142 loop : -0.33 (0.36), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 47 HIS 0.002 0.001 HIS R 505 PHE 0.011 0.001 PHE L 91 TYR 0.024 0.002 TYR L 49 ARG 0.003 0.001 ARG R 403 *********************** 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 54 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 43 time to evaluate : 0.374 Fit side-chains REVERT: H 43 LYS cc_start: 0.8711 (mmtp) cc_final: 0.8392 (mttm) REVERT: H 108 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8841 (tt) REVERT: R 501 TYR cc_start: 0.7518 (m-10) cc_final: 0.7287 (m-10) outliers start: 11 outliers final: 7 residues processed: 51 average time/residue: 0.1392 time to fit residues: 8.9996 Evaluate side-chains 52 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 44 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 50 ASP Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 415 THR Chi-restraints excluded: chain R residue 470 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 16 optimal weight: 0.0970 chunk 33 optimal weight: 0.3980 chunk 27 optimal weight: 0.0040 chunk 20 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 7 optimal weight: 0.2980 overall best weight: 0.2790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 100JGLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3408 Z= 0.174 Angle : 0.504 5.003 4635 Z= 0.266 Chirality : 0.043 0.147 511 Planarity : 0.005 0.043 596 Dihedral : 5.476 53.088 489 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.63 % Allowed : 16.58 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.43 (0.39), residues: 419 helix: -3.71 (0.74), residues: 25 sheet: 0.39 (0.45), residues: 142 loop : -0.25 (0.36), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.001 0.000 HIS R 505 PHE 0.007 0.001 PHE L 91 TYR 0.014 0.001 TYR L 49 ARG 0.003 0.000 ARG R 403 *********************** 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 58 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 52 time to evaluate : 0.377 Fit side-chains REVERT: H 43 LYS cc_start: 0.8701 (mmtp) cc_final: 0.8310 (mttm) REVERT: L 79 GLN cc_start: 0.7638 (mp10) cc_final: 0.7151 (mt0) outliers start: 6 outliers final: 4 residues processed: 55 average time/residue: 0.1632 time to fit residues: 11.0706 Evaluate side-chains 55 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 51 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 50 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain R residue 470 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 0.4980 chunk 13 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 38 optimal weight: 0.0470 chunk 4 optimal weight: 0.0980 chunk 22 optimal weight: 0.5980 overall best weight: 0.3878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 100JGLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3408 Z= 0.200 Angle : 0.506 5.634 4635 Z= 0.268 Chirality : 0.044 0.147 511 Planarity : 0.005 0.042 596 Dihedral : 5.469 52.998 489 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.45 % Allowed : 17.66 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.43 (0.39), residues: 419 helix: -3.72 (0.74), residues: 25 sheet: 0.40 (0.45), residues: 142 loop : -0.25 (0.36), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.003 0.001 HIS R 505 PHE 0.007 0.001 PHE L 91 TYR 0.017 0.001 TYR L 49 ARG 0.007 0.000 ARG R 403 *********************** 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 58 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 49 time to evaluate : 0.383 Fit side-chains REVERT: H 82 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7923 (mtp) REVERT: L 79 GLN cc_start: 0.7689 (mp10) cc_final: 0.7203 (mt0) outliers start: 9 outliers final: 6 residues processed: 54 average time/residue: 0.1626 time to fit residues: 10.8325 Evaluate side-chains 55 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 48 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 50 ASP Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain R residue 415 THR Chi-restraints excluded: chain R residue 470 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 24 optimal weight: 0.0980 chunk 18 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 11 optimal weight: 0.0040 chunk 7 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 100JGLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 505 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3408 Z= 0.239 Angle : 0.515 5.902 4635 Z= 0.274 Chirality : 0.045 0.151 511 Planarity : 0.005 0.040 596 Dihedral : 5.547 53.069 489 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.90 % Allowed : 18.21 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.38 (0.39), residues: 419 helix: -3.76 (0.73), residues: 25 sheet: 0.44 (0.47), residues: 133 loop : -0.19 (0.35), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 47 HIS 0.002 0.001 HIS R 505 PHE 0.008 0.001 PHE L 91 TYR 0.019 0.002 TYR L 49 ARG 0.007 0.001 ARG R 403 *********************** 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 53 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 46 time to evaluate : 0.357 Fit side-chains REVERT: H 82 MET cc_start: 0.8283 (OUTLIER) cc_final: 0.7937 (mtp) REVERT: L 79 GLN cc_start: 0.7614 (mp10) cc_final: 0.7136 (mt0) REVERT: R 386 LYS cc_start: 0.7954 (pttt) cc_final: 0.7637 (ptpp) outliers start: 7 outliers final: 5 residues processed: 50 average time/residue: 0.1479 time to fit residues: 9.2876 Evaluate side-chains 54 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 48 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain R residue 415 THR Chi-restraints excluded: chain R residue 470 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.3980 chunk 19 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 34 optimal weight: 0.0070 chunk 36 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 100JGLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3408 Z= 0.231 Angle : 0.512 5.808 4635 Z= 0.273 Chirality : 0.044 0.150 511 Planarity : 0.005 0.039 596 Dihedral : 5.553 53.156 489 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.45 % Allowed : 17.93 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.31 (0.39), residues: 419 helix: -3.09 (0.89), residues: 19 sheet: 0.38 (0.45), residues: 146 loop : -0.27 (0.36), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 47 HIS 0.002 0.001 HIS R 505 PHE 0.008 0.001 PHE L 91 TYR 0.018 0.001 TYR L 49 ARG 0.004 0.000 ARG R 403 *********************** 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 51 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 42 time to evaluate : 0.400 Fit side-chains REVERT: H 43 LYS cc_start: 0.8664 (mmtp) cc_final: 0.8184 (mttm) REVERT: H 82 MET cc_start: 0.8324 (OUTLIER) cc_final: 0.7954 (mtp) REVERT: L 79 GLN cc_start: 0.7669 (mp10) cc_final: 0.7245 (mt0) REVERT: R 386 LYS cc_start: 0.7926 (pttt) cc_final: 0.7627 (ptpp) outliers start: 9 outliers final: 7 residues processed: 48 average time/residue: 0.1667 time to fit residues: 10.1584 Evaluate side-chains 52 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 44 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain R residue 415 THR Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain R residue 470 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 0.3980 chunk 33 optimal weight: 0.0040 chunk 34 optimal weight: 0.4980 chunk 36 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 18 optimal weight: 0.0970 chunk 27 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 overall best weight: 0.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 100JGLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3408 Z= 0.176 Angle : 0.484 5.384 4635 Z= 0.257 Chirality : 0.043 0.146 511 Planarity : 0.004 0.038 596 Dihedral : 5.401 53.214 489 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.17 % Allowed : 19.02 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.32 (0.39), residues: 419 helix: -3.69 (0.75), residues: 25 sheet: 0.49 (0.45), residues: 139 loop : -0.17 (0.36), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.001 0.001 HIS R 505 PHE 0.007 0.001 PHE L 91 TYR 0.014 0.001 TYR L 49 ARG 0.003 0.000 ARG R 403 *********************** 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 56 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 48 time to evaluate : 0.350 Fit side-chains REVERT: H 43 LYS cc_start: 0.8665 (mmtp) cc_final: 0.8186 (mttp) REVERT: H 82 MET cc_start: 0.8358 (OUTLIER) cc_final: 0.7951 (mtp) REVERT: L 79 GLN cc_start: 0.7632 (mp10) cc_final: 0.7170 (mt0) REVERT: R 501 TYR cc_start: 0.7460 (m-10) cc_final: 0.7122 (m-10) outliers start: 8 outliers final: 6 residues processed: 53 average time/residue: 0.1476 time to fit residues: 9.8507 Evaluate side-chains 55 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 48 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain R residue 470 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 4 optimal weight: 0.1980 chunk 13 optimal weight: 0.0370 chunk 33 optimal weight: 0.4980 chunk 6 optimal weight: 0.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 100JGLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3408 Z= 0.249 Angle : 0.516 5.920 4635 Z= 0.275 Chirality : 0.044 0.149 511 Planarity : 0.005 0.038 596 Dihedral : 5.533 53.131 489 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.45 % Allowed : 18.75 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.39 (0.39), residues: 419 helix: -3.75 (0.72), residues: 25 sheet: 0.38 (0.46), residues: 133 loop : -0.17 (0.35), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 47 HIS 0.001 0.000 HIS R 505 PHE 0.007 0.001 PHE L 91 TYR 0.019 0.002 TYR L 49 ARG 0.004 0.000 ARG R 403 ********************** 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 55 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 46 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: H 43 LYS cc_start: 0.8677 (mmtp) cc_final: 0.8208 (mttp) REVERT: H 82 MET cc_start: 0.8374 (OUTLIER) cc_final: 0.8013 (mtp) REVERT: R 414 GLN cc_start: 0.9091 (mm-40) cc_final: 0.8792 (mm-40) outliers start: 9 outliers final: 6 residues processed: 52 average time/residue: 0.1434 time to fit residues: 9.4913 Evaluate side-chains 54 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 47 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 470 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 0.0980 chunk 21 optimal weight: 0.6980 chunk 27 optimal weight: 0.0870 chunk 26 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 100JGLN ** 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 = 0.3846 r_free = 0.3846 target = 0.163626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.127696 restraints weight = 3543.437| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.06 r_work: 0.3157 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3408 Z= 0.221 Angle : 0.508 5.662 4635 Z= 0.271 Chirality : 0.044 0.150 511 Planarity : 0.005 0.037 596 Dihedral : 5.516 53.150 489 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.17 % Allowed : 19.57 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.34 (0.39), residues: 419 helix: -3.74 (0.73), residues: 25 sheet: 0.38 (0.45), residues: 142 loop : -0.12 (0.36), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 47 HIS 0.001 0.001 HIS R 505 PHE 0.007 0.001 PHE L 91 TYR 0.017 0.001 TYR L 49 ARG 0.004 0.000 ARG R 403 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1406.58 seconds wall clock time: 25 minutes 44.68 seconds (1544.68 seconds total)