Starting phenix.real_space_refine on Wed Jan 17 13:19:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcx_38258/01_2024/8xcx_38258_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcx_38258/01_2024/8xcx_38258.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcx_38258/01_2024/8xcx_38258_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcx_38258/01_2024/8xcx_38258_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcx_38258/01_2024/8xcx_38258_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcx_38258/01_2024/8xcx_38258.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcx_38258/01_2024/8xcx_38258.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcx_38258/01_2024/8xcx_38258_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcx_38258/01_2024/8xcx_38258_neut_updated.pdb" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 14 5.16 5 C 2100 2.51 5 N 563 2.21 5 O 649 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 78": "OE1" <-> "OE2" Residue "A TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 244": "OD1" <-> "OD2" Residue "A GLU 332": "OE1" <-> "OE2" Residue "A ASP 340": "OD1" <-> "OD2" Residue "A GLU 367": "OE1" <-> "OE2" Residue "A ASP 390": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 3329 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3263 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 416, 3255 Classifications: {'peptide': 416} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 395} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Conformer: "B" Number of residues, atoms: 416, 3255 Classifications: {'peptide': 416} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 395} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 bond proxies already assigned to first conformer: 3319 Chain: "A" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 66 Unusual residues: {'NAP': 1} Classifications: {'peptide': 1, 'undetermined': 1, 'water': 25} Link IDs: {None: 26} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'NAP:plan-2': 1, 'NAP:plan-4': 1} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 4.00, per 1000 atoms: 1.20 Number of scatterers: 3329 At special positions: 0 Unit cell: (68.432, 72.944, 72.192, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 3 15.00 O 649 8.00 N 563 7.00 C 2100 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 1.27 Conformation dependent library (CDL) restraints added in 1.3 seconds 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 762 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 16 helices and 3 sheets defined 48.1% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 6 through 20 removed outlier: 3.922A pdb=" N TYR A 20 " --> pdb=" O ARG A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 31 Processing helix chain 'A' and resid 80 through 96 removed outlier: 3.529A pdb=" N TRP A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 114 No H-bonds generated for 'chain 'A' and resid 112 through 114' Processing helix chain 'A' and resid 117 through 134 removed outlier: 5.725A pdb=" N ASP A 133 " --> pdb=" O ARG A 129 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N VAL A 134 " --> pdb=" O ALA A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 Processing helix chain 'A' and resid 170 through 173 Processing helix chain 'A' and resid 190 through 206 Processing helix chain 'A' and resid 222 through 234 Processing helix chain 'A' and resid 257 through 267 Processing helix chain 'A' and resid 281 through 286 removed outlier: 3.853A pdb=" N GLU A 286 " --> pdb=" O GLU A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 332 Processing helix chain 'A' and resid 340 through 343 No H-bonds generated for 'chain 'A' and resid 340 through 343' Processing helix chain 'A' and resid 346 through 360 Processing helix chain 'A' and resid 366 through 391 Processing helix chain 'A' and resid 395 through 414 Processing sheet with id= A, first strand: chain 'A' and resid 36 through 45 removed outlier: 4.722A pdb=" N THR A 55 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLY A 103 " --> pdb=" O HIS A 61 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 291 through 294 removed outlier: 6.458A pdb=" N THR A 238 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N VAL A 217 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N VAL A 240 " --> pdb=" O VAL A 217 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 313 through 315 removed outlier: 6.730A pdb=" N LEU A 336 " --> pdb=" O VAL A 314 " (cutoff:3.500A) No H-bonds generated for sheet with id= C 162 hydrogen bonds defined for protein. 471 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: 1.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1070 1.34 - 1.46: 662 1.46 - 1.58: 1618 1.58 - 1.69: 2 1.69 - 1.81: 27 Bond restraints: 3379 Sorted by residual: bond pdb=" O2B NAP A 500 " pdb=" P2B NAP A 500 " ideal model delta sigma weight residual 1.736 1.568 0.168 2.00e-02 2.50e+03 7.09e+01 bond pdb=" N ARG A 187 " pdb=" CA BARG A 187 " ideal model delta sigma weight residual 1.457 1.545 -0.088 1.32e-02 5.74e+03 4.43e+01 bond pdb=" C4A NAP A 500 " pdb=" N3A NAP A 500 " ideal model delta sigma weight residual 1.332 1.441 -0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" C6A NAP A 500 " pdb=" N6A NAP A 500 " ideal model delta sigma weight residual 1.335 1.435 -0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" C8A NAP A 500 " pdb=" N7A NAP A 500 " ideal model delta sigma weight residual 1.301 1.397 -0.096 2.00e-02 2.50e+03 2.32e+01 ... (remaining 3374 not shown) Histogram of bond angle deviations from ideal: 99.28 - 106.23: 94 106.23 - 113.18: 1850 113.18 - 120.14: 1173 120.14 - 127.09: 1419 127.09 - 134.04: 53 Bond angle restraints: 4589 Sorted by residual: angle pdb=" C ASP A 5 " pdb=" N PRO A 6 " pdb=" CA PRO A 6 " ideal model delta sigma weight residual 119.84 127.09 -7.25 1.25e+00 6.40e-01 3.37e+01 angle pdb=" N ARG A 187 " pdb=" CA BARG A 187 " pdb=" C ARG A 187 " ideal model delta sigma weight residual 113.20 119.56 -6.36 1.21e+00 6.83e-01 2.76e+01 angle pdb=" N ARG A 187 " pdb=" CA AARG A 187 " pdb=" C ARG A 187 " ideal model delta sigma weight residual 113.20 118.36 -5.16 1.21e+00 6.83e-01 1.82e+01 angle pdb=" O1A NAP A 500 " pdb=" PA NAP A 500 " pdb=" O2A NAP A 500 " ideal model delta sigma weight residual 121.77 109.71 12.06 3.00e+00 1.11e-01 1.62e+01 angle pdb=" O1N NAP A 500 " pdb=" PN NAP A 500 " pdb=" O2N NAP A 500 " ideal model delta sigma weight residual 122.51 110.62 11.89 3.00e+00 1.11e-01 1.57e+01 ... (remaining 4584 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 1802 17.55 - 35.09: 173 35.09 - 52.64: 44 52.64 - 70.19: 17 70.19 - 87.74: 7 Dihedral angle restraints: 2043 sinusoidal: 848 harmonic: 1195 Sorted by residual: dihedral pdb=" CB GLU A 78 " pdb=" CG GLU A 78 " pdb=" CD GLU A 78 " pdb=" OE1 GLU A 78 " ideal model delta sinusoidal sigma weight residual 0.00 -84.53 84.53 1 3.00e+01 1.11e-03 9.65e+00 dihedral pdb=" N ASP A 5 " pdb=" CA ASP A 5 " pdb=" CB ASP A 5 " pdb=" CG ASP A 5 " ideal model delta sinusoidal sigma weight residual -60.00 -115.98 55.98 3 1.50e+01 4.44e-03 9.38e+00 dihedral pdb=" CB LYS A 264 " pdb=" CG LYS A 264 " pdb=" CD LYS A 264 " pdb=" CE LYS A 264 " ideal model delta sinusoidal sigma weight residual 180.00 124.52 55.48 3 1.50e+01 4.44e-03 9.35e+00 ... (remaining 2040 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 418 0.060 - 0.119: 74 0.119 - 0.179: 5 0.179 - 0.239: 1 0.239 - 0.298: 1 Chirality restraints: 499 Sorted by residual: chirality pdb=" C2B NAP A 500 " pdb=" C1B NAP A 500 " pdb=" C3B NAP A 500 " pdb=" O2B NAP A 500 " both_signs ideal model delta sigma weight residual False -2.75 -2.46 -0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CA AARG A 187 " pdb=" N ARG A 187 " pdb=" C ARG A 187 " pdb=" CB AARG A 187 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.27e-01 chirality pdb=" CB VAL A 97 " pdb=" CA VAL A 97 " pdb=" CG1 VAL A 97 " pdb=" CG2 VAL A 97 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.25e-01 ... (remaining 496 not shown) Planarity restraints: 584 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD BARG A 187 " 0.189 9.50e-02 1.11e+02 8.49e-02 4.42e+00 pdb=" NE BARG A 187 " -0.011 2.00e-02 2.50e+03 pdb=" CZ BARG A 187 " -0.002 2.00e-02 2.50e+03 pdb=" NH1BARG A 187 " -0.002 2.00e-02 2.50e+03 pdb=" NH2BARG A 187 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 149 " -0.032 5.00e-02 4.00e+02 4.87e-02 3.80e+00 pdb=" N PRO A 150 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 150 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 150 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 141 " 0.026 5.00e-02 4.00e+02 3.87e-02 2.40e+00 pdb=" N PRO A 142 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 142 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 142 " 0.022 5.00e-02 4.00e+02 ... (remaining 581 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 1288 2.90 - 3.40: 3333 3.40 - 3.90: 5915 3.90 - 4.40: 6855 4.40 - 4.90: 11179 Nonbonded interactions: 28570 Sorted by model distance: nonbonded pdb=" N THR A 280 " pdb=" OE2 GLU A 283 " model vdw 2.405 2.520 nonbonded pdb=" O ALA A 223 " pdb=" OG1 THR A 227 " model vdw 2.442 2.440 nonbonded pdb=" O LYS A 213 " pdb=" N THR A 238 " model vdw 2.458 2.520 nonbonded pdb=" NZ LYS A 69 " pdb=" OG1 THR A 175 " model vdw 2.518 2.520 nonbonded pdb=" O ASP A 413 " pdb=" O HOH A 601 " model vdw 2.519 2.440 ... (remaining 28565 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 0.740 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: 3.530 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 16.650 Find NCS groups from input model: 0.090 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:12.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 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 : 0.008 0.168 3379 Z= 0.548 Angle : 0.836 12.060 4589 Z= 0.447 Chirality : 0.047 0.298 499 Planarity : 0.006 0.085 584 Dihedral : 16.535 87.736 1281 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.96 % Allowed : 1.48 % Favored : 95.56 % 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: 1.08 (0.43), residues: 415 helix: 2.09 (0.35), residues: 208 sheet: -1.12 (0.58), residues: 75 loop : -0.28 (0.59), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 63 HIS 0.005 0.001 HIS A 388 PHE 0.009 0.001 PHE A 341 TYR 0.010 0.001 TYR A 363 ARG 0.001 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 58 time to evaluate : 0.366 Fit side-chains REVERT: A 113 LYS cc_start: 0.7761 (OUTLIER) cc_final: 0.7249 (ttpt) REVERT: A 256 ASP cc_start: 0.7727 (OUTLIER) cc_final: 0.7056 (t70) outliers start: 9 outliers final: 0 residues processed: 64 average time/residue: 1.4807 time to fit residues: 97.0760 Evaluate side-chains 53 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 51 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 256 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 3.9990 chunk 31 optimal weight: 0.0670 chunk 17 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 20 optimal weight: 8.9990 chunk 16 optimal weight: 0.4980 chunk 32 optimal weight: 40.0000 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 23 optimal weight: 8.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 281 ASN A 388 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3379 Z= 0.152 Angle : 0.480 5.325 4589 Z= 0.250 Chirality : 0.043 0.163 499 Planarity : 0.004 0.047 584 Dihedral : 11.381 61.245 501 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.37 % Allowed : 9.76 % Favored : 87.87 % 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: 1.61 (0.43), residues: 415 helix: 2.37 (0.35), residues: 208 sheet: -0.60 (0.63), residues: 70 loop : 0.01 (0.57), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 63 HIS 0.002 0.001 HIS A 388 PHE 0.008 0.001 PHE A 341 TYR 0.022 0.001 TYR A 250 ARG 0.001 0.000 ARG A 73 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 52 time to evaluate : 0.377 Fit side-chains REVERT: A 246 ARG cc_start: 0.4895 (OUTLIER) cc_final: 0.3868 (tpt170) REVERT: A 256 ASP cc_start: 0.7741 (OUTLIER) cc_final: 0.6936 (t70) outliers start: 7 outliers final: 1 residues processed: 56 average time/residue: 1.5806 time to fit residues: 90.6174 Evaluate side-chains 53 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 50 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 256 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 25 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 29 optimal weight: 8.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 281 ASN A 388 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3379 Z= 0.243 Angle : 0.499 6.455 4589 Z= 0.260 Chirality : 0.044 0.157 499 Planarity : 0.004 0.048 584 Dihedral : 10.896 57.634 497 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.48 % Allowed : 10.95 % Favored : 87.57 % 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: 1.58 (0.42), residues: 415 helix: 2.32 (0.35), residues: 207 sheet: -0.48 (0.63), residues: 70 loop : -0.00 (0.56), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 63 HIS 0.001 0.001 HIS A 61 PHE 0.010 0.001 PHE A 341 TYR 0.010 0.001 TYR A 363 ARG 0.001 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 50 time to evaluate : 0.415 Fit side-chains REVERT: A 246 ARG cc_start: 0.4989 (OUTLIER) cc_final: 0.3898 (tpt170) REVERT: A 256 ASP cc_start: 0.7818 (OUTLIER) cc_final: 0.7462 (t70) outliers start: 5 outliers final: 1 residues processed: 55 average time/residue: 1.5786 time to fit residues: 88.9422 Evaluate side-chains 52 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 49 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 256 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 6.9990 chunk 28 optimal weight: 9.9990 chunk 19 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 25 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 10 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN A 388 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3379 Z= 0.199 Angle : 0.470 5.785 4589 Z= 0.245 Chirality : 0.043 0.143 499 Planarity : 0.004 0.048 584 Dihedral : 10.173 53.032 497 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.48 % Allowed : 12.72 % Favored : 85.80 % 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: 1.57 (0.42), residues: 415 helix: 2.36 (0.34), residues: 207 sheet: -0.70 (0.61), residues: 73 loop : 0.06 (0.57), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.002 0.001 HIS A 388 PHE 0.009 0.001 PHE A 381 TYR 0.016 0.001 TYR A 250 ARG 0.001 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 48 time to evaluate : 0.431 Fit side-chains REVERT: A 246 ARG cc_start: 0.4966 (OUTLIER) cc_final: 0.3884 (tpt170) REVERT: A 256 ASP cc_start: 0.7863 (OUTLIER) cc_final: 0.7520 (t70) outliers start: 5 outliers final: 0 residues processed: 51 average time/residue: 1.5858 time to fit residues: 82.9162 Evaluate side-chains 50 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 48 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 256 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 16 optimal weight: 0.8980 chunk 33 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 13 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN A 388 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3379 Z= 0.217 Angle : 0.475 5.656 4589 Z= 0.247 Chirality : 0.044 0.140 499 Planarity : 0.004 0.049 584 Dihedral : 9.777 53.651 497 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.07 % Allowed : 12.72 % Favored : 85.21 % 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: 1.49 (0.42), residues: 415 helix: 2.32 (0.34), residues: 207 sheet: -0.79 (0.61), residues: 75 loop : 0.04 (0.57), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.003 0.001 HIS A 388 PHE 0.009 0.001 PHE A 381 TYR 0.010 0.001 TYR A 363 ARG 0.001 0.000 ARG A 406 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 48 time to evaluate : 0.383 Fit side-chains REVERT: A 246 ARG cc_start: 0.4998 (OUTLIER) cc_final: 0.3813 (tpt170) REVERT: A 256 ASP cc_start: 0.7921 (OUTLIER) cc_final: 0.7610 (t70) outliers start: 7 outliers final: 2 residues processed: 51 average time/residue: 1.5145 time to fit residues: 79.1221 Evaluate side-chains 53 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 49 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain A residue 281 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 6.9990 chunk 9 optimal weight: 0.0060 chunk 39 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 18 optimal weight: 0.2980 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 overall best weight: 1.2400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN A 388 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3379 Z= 0.171 Angle : 0.453 4.660 4589 Z= 0.235 Chirality : 0.043 0.127 499 Planarity : 0.004 0.049 584 Dihedral : 9.261 60.120 497 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.48 % Allowed : 13.61 % Favored : 84.91 % 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: 1.58 (0.42), residues: 415 helix: 2.39 (0.34), residues: 207 sheet: -0.74 (0.61), residues: 75 loop : 0.07 (0.56), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.002 0.001 HIS A 388 PHE 0.008 0.001 PHE A 381 TYR 0.008 0.001 TYR A 363 ARG 0.001 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 48 time to evaluate : 0.321 Fit side-chains REVERT: A 246 ARG cc_start: 0.5008 (OUTLIER) cc_final: 0.3750 (tpt170) outliers start: 5 outliers final: 2 residues processed: 51 average time/residue: 1.5441 time to fit residues: 80.6867 Evaluate side-chains 50 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 47 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 281 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 0.1980 chunk 39 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3379 Z= 0.172 Angle : 0.454 5.206 4589 Z= 0.235 Chirality : 0.043 0.132 499 Planarity : 0.004 0.049 584 Dihedral : 8.980 65.461 495 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.78 % Allowed : 14.20 % Favored : 84.02 % 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: 1.61 (0.42), residues: 415 helix: 2.39 (0.34), residues: 208 sheet: -0.72 (0.62), residues: 75 loop : 0.12 (0.56), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.002 0.001 HIS A 388 PHE 0.008 0.001 PHE A 341 TYR 0.008 0.001 TYR A 363 ARG 0.001 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 46 time to evaluate : 0.396 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 49 average time/residue: 1.5444 time to fit residues: 77.6961 Evaluate side-chains 49 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 46 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 281 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 31 optimal weight: 8.9990 chunk 35 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 22 optimal weight: 10.0000 chunk 16 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3379 Z= 0.198 Angle : 0.474 6.957 4589 Z= 0.242 Chirality : 0.043 0.131 499 Planarity : 0.004 0.049 584 Dihedral : 8.862 69.619 495 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.48 % Allowed : 15.38 % Favored : 83.14 % 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: 1.59 (0.42), residues: 415 helix: 2.36 (0.34), residues: 208 sheet: -0.71 (0.61), residues: 75 loop : 0.11 (0.56), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.002 0.001 HIS A 388 PHE 0.009 0.001 PHE A 341 TYR 0.009 0.001 TYR A 363 ARG 0.001 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 46 time to evaluate : 0.385 Fit side-chains REVERT: A 246 ARG cc_start: 0.5039 (OUTLIER) cc_final: 0.3790 (tpt170) outliers start: 5 outliers final: 3 residues processed: 49 average time/residue: 1.5399 time to fit residues: 77.4356 Evaluate side-chains 49 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 45 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 281 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 38 optimal weight: 8.9990 chunk 23 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 27 optimal weight: 0.0670 chunk 40 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.9122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3379 Z= 0.154 Angle : 0.450 4.876 4589 Z= 0.233 Chirality : 0.043 0.147 499 Planarity : 0.004 0.048 584 Dihedral : 8.491 76.211 495 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.18 % Allowed : 15.68 % Favored : 83.14 % 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: 1.64 (0.42), residues: 415 helix: 2.40 (0.34), residues: 208 sheet: -0.72 (0.61), residues: 75 loop : 0.17 (0.56), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.002 0.001 HIS A 388 PHE 0.007 0.001 PHE A 341 TYR 0.007 0.001 TYR A 363 ARG 0.001 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 45 time to evaluate : 0.347 Fit side-chains REVERT: A 246 ARG cc_start: 0.4986 (OUTLIER) cc_final: 0.3829 (tpt170) outliers start: 4 outliers final: 2 residues processed: 47 average time/residue: 1.5497 time to fit residues: 74.6918 Evaluate side-chains 48 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 45 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 281 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.4980 chunk 3 optimal weight: 0.9990 chunk 25 optimal weight: 8.9990 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 29 optimal weight: 0.0770 chunk 4 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.6742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3379 Z= 0.145 Angle : 0.442 4.348 4589 Z= 0.227 Chirality : 0.042 0.134 499 Planarity : 0.004 0.048 584 Dihedral : 8.257 82.806 495 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.48 % Allowed : 15.38 % Favored : 83.14 % 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: 1.68 (0.42), residues: 415 helix: 2.41 (0.34), residues: 208 sheet: -0.66 (0.62), residues: 75 loop : 0.19 (0.56), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 63 HIS 0.002 0.001 HIS A 388 PHE 0.007 0.001 PHE A 341 TYR 0.007 0.001 TYR A 363 ARG 0.001 0.000 ARG A 16 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 44 time to evaluate : 0.351 Fit side-chains REVERT: A 246 ARG cc_start: 0.5011 (OUTLIER) cc_final: 0.3852 (tpt170) outliers start: 5 outliers final: 3 residues processed: 48 average time/residue: 1.6184 time to fit residues: 79.6122 Evaluate side-chains 48 residues out of total 338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 44 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 280 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.9980 chunk 1 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 21 optimal weight: 10.0000 chunk 27 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 16 optimal weight: 0.1980 chunk 15 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.136706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.098712 restraints weight = 9947.209| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 2.51 r_work: 0.2774 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2722 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2722 r_free = 0.2722 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2722 r_free = 0.2722 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2722 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3379 Z= 0.164 Angle : 0.453 5.326 4589 Z= 0.232 Chirality : 0.043 0.123 499 Planarity : 0.004 0.049 584 Dihedral : 8.202 86.334 495 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.48 % Allowed : 15.09 % Favored : 83.43 % 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: 1.67 (0.42), residues: 415 helix: 2.41 (0.34), residues: 208 sheet: -0.70 (0.61), residues: 75 loop : 0.21 (0.56), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 63 HIS 0.002 0.001 HIS A 388 PHE 0.008 0.001 PHE A 341 TYR 0.008 0.001 TYR A 363 ARG 0.001 0.000 ARG A 16 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1931.82 seconds wall clock time: 35 minutes 6.51 seconds (2106.51 seconds total)