Starting phenix.real_space_refine on Tue Feb 13 08:03:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8do0_27586/02_2024/8do0_27586_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8do0_27586/02_2024/8do0_27586.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8do0_27586/02_2024/8do0_27586_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8do0_27586/02_2024/8do0_27586_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8do0_27586/02_2024/8do0_27586_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8do0_27586/02_2024/8do0_27586.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8do0_27586/02_2024/8do0_27586.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8do0_27586/02_2024/8do0_27586_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8do0_27586/02_2024/8do0_27586_trim_updated.pdb" } resolution = 2.86 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= 0.003 sd= 0.043 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 26 5.16 5 C 2819 2.51 5 N 672 2.21 5 O 730 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 4247 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 474 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 57} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "C" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 251 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 29} Chain: "A" Number of atoms: 3522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3522 Unusual residues: {'Q6B': 1} Classifications: {'peptide': 449, 'undetermined': 1, 'water': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 18, 'TRANS': 430, None: 2} Not linked: pdbres="VAL A 468 " pdbres="Q6B A 501 " Not linked: pdbres="Q6B A 501 " pdbres="HOH A 601 " Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 2.91, per 1000 atoms: 0.69 Number of scatterers: 4247 At special positions: 0 Unit cell: (95.55, 84, 78.75, 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 26 16.00 O 730 8.00 N 672 7.00 C 2819 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.70 Conformation dependent library (CDL) restraints added in 713.1 milliseconds 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 994 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 20 helices and 1 sheets defined 66.8% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'B' and resid 8 through 24 Processing helix chain 'B' and resid 30 through 65 removed outlier: 3.756A pdb=" N LYS B 35 " --> pdb=" O LYS B 31 " (cutoff:3.500A) Proline residue: B 60 - end of helix Processing helix chain 'C' and resid 70 through 95 Processing helix chain 'A' and resid 11 through 14 removed outlier: 3.768A pdb=" N VAL A 14 " --> pdb=" O PRO A 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 11 through 14' Processing helix chain 'A' and resid 28 through 47 Processing helix chain 'A' and resid 63 through 65 No H-bonds generated for 'chain 'A' and resid 63 through 65' Processing helix chain 'A' and resid 82 through 97 Processing helix chain 'A' and resid 108 through 133 Processing helix chain 'A' and resid 140 through 170 removed outlier: 3.786A pdb=" N GLY A 144 " --> pdb=" O PRO A 140 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N ALA A 145 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N GLY A 146 " --> pdb=" O GLU A 142 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ILE A 147 " --> pdb=" O MET A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 196 Processing helix chain 'A' and resid 212 through 222 Processing helix chain 'A' and resid 226 through 234 Processing helix chain 'A' and resid 242 through 260 Processing helix chain 'A' and resid 289 through 311 Processing helix chain 'A' and resid 316 through 321 Processing helix chain 'A' and resid 351 through 356 Processing helix chain 'A' and resid 358 through 382 removed outlier: 3.884A pdb=" N GLU A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 397 Processing helix chain 'A' and resid 409 through 437 Proline residue: A 418 - end of helix Processing helix chain 'A' and resid 443 through 467 Processing sheet with id= A, first strand: chain 'A' and resid 262 through 267 removed outlier: 3.568A pdb=" N ILE A 267 " --> pdb=" O GLY A 277 " (cutoff:3.500A) 276 hydrogen bonds defined for protein. 825 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.16 Time building geometry restraints manager: 1.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 670 1.32 - 1.45: 1108 1.45 - 1.57: 2514 1.57 - 1.69: 0 1.69 - 1.81: 43 Bond restraints: 4335 Sorted by residual: bond pdb=" C06 Q6B A 501 " pdb=" C07 Q6B A 501 " ideal model delta sigma weight residual 1.596 1.325 0.271 2.00e-02 2.50e+03 1.83e+02 bond pdb=" C19 Q6B A 501 " pdb=" C20 Q6B A 501 " ideal model delta sigma weight residual 1.554 1.407 0.147 2.00e-02 2.50e+03 5.42e+01 bond pdb=" C21 Q6B A 501 " pdb=" C22 Q6B A 501 " ideal model delta sigma weight residual 1.562 1.447 0.115 2.00e-02 2.50e+03 3.31e+01 bond pdb=" C17 Q6B A 501 " pdb=" C18 Q6B A 501 " ideal model delta sigma weight residual 1.573 1.462 0.111 2.00e-02 2.50e+03 3.10e+01 bond pdb=" C05 Q6B A 501 " pdb=" C06 Q6B A 501 " ideal model delta sigma weight residual 1.604 1.502 0.102 2.00e-02 2.50e+03 2.58e+01 ... (remaining 4330 not shown) Histogram of bond angle deviations from ideal: 100.64 - 107.31: 132 107.31 - 113.98: 2520 113.98 - 120.65: 1818 120.65 - 127.32: 1361 127.32 - 133.99: 38 Bond angle restraints: 5869 Sorted by residual: angle pdb=" C22 Q6B A 501 " pdb=" C23 Q6B A 501 " pdb=" C24 Q6B A 501 " ideal model delta sigma weight residual 85.87 128.46 -42.59 3.00e+00 1.11e-01 2.02e+02 angle pdb=" C18 Q6B A 501 " pdb=" C19 Q6B A 501 " pdb=" C20 Q6B A 501 " ideal model delta sigma weight residual 85.88 127.03 -41.15 3.00e+00 1.11e-01 1.88e+02 angle pdb=" C12 Q6B A 501 " pdb=" C14 Q6B A 501 " pdb=" C15 Q6B A 501 " ideal model delta sigma weight residual 85.86 122.15 -36.29 3.00e+00 1.11e-01 1.46e+02 angle pdb=" C17 Q6B A 501 " pdb=" C18 Q6B A 501 " pdb=" C33 Q6B A 501 " ideal model delta sigma weight residual 92.59 119.41 -26.82 3.00e+00 1.11e-01 7.99e+01 angle pdb=" C20 Q6B A 501 " pdb=" C21 Q6B A 501 " pdb=" C22 Q6B A 501 " ideal model delta sigma weight residual 152.67 127.18 25.49 3.00e+00 1.11e-01 7.22e+01 ... (remaining 5864 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.25: 2454 25.25 - 50.49: 83 50.49 - 75.74: 8 75.74 - 100.98: 7 100.98 - 126.23: 4 Dihedral angle restraints: 2556 sinusoidal: 1007 harmonic: 1549 Sorted by residual: dihedral pdb=" C36 Q6B A 501 " pdb=" C02 Q6B A 501 " pdb=" C37 Q6B A 501 " pdb=" O03 Q6B A 501 " ideal model delta sinusoidal sigma weight residual 198.53 72.30 126.23 1 3.00e+01 1.11e-03 1.70e+01 dihedral pdb=" C08 Q6B A 501 " pdb=" C09 Q6B A 501 " pdb=" C10 Q6B A 501 " pdb=" C35 Q6B A 501 " ideal model delta sinusoidal sigma weight residual 63.94 -54.80 118.74 1 3.00e+01 1.11e-03 1.58e+01 dihedral pdb=" C04 Q6B A 501 " pdb=" C02 Q6B A 501 " pdb=" O03 Q6B A 501 " pdb=" C37 Q6B A 501 " ideal model delta sinusoidal sigma weight residual 83.01 -162.69 -114.30 1 3.00e+01 1.11e-03 1.51e+01 ... (remaining 2553 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 504 0.040 - 0.080: 157 0.080 - 0.120: 35 0.120 - 0.160: 0 0.160 - 0.200: 3 Chirality restraints: 699 Sorted by residual: chirality pdb=" C45 Q6B A 501 " pdb=" C44 Q6B A 501 " pdb=" C46 Q6B A 501 " pdb=" C47 Q6B A 501 " both_signs ideal model delta sigma weight residual False -2.77 -2.57 -0.20 2.00e-01 2.50e+01 9.95e-01 chirality pdb=" C09 Q6B A 501 " pdb=" C08 Q6B A 501 " pdb=" C10 Q6B A 501 " pdb=" C38 Q6B A 501 " both_signs ideal model delta sigma weight residual False -2.77 -2.58 -0.19 2.00e-01 2.50e+01 9.08e-01 chirality pdb=" C40 Q6B A 501 " pdb=" C04 Q6B A 501 " pdb=" C41 Q6B A 501 " pdb=" C42 Q6B A 501 " both_signs ideal model delta sigma weight residual False -2.77 -2.58 -0.19 2.00e-01 2.50e+01 8.62e-01 ... (remaining 696 not shown) Planarity restraints: 718 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C21 Q6B A 501 " -0.066 2.00e-02 2.50e+03 6.23e-02 4.85e+01 pdb=" C22 Q6B A 501 " 0.054 2.00e-02 2.50e+03 pdb=" C23 Q6B A 501 " 0.086 2.00e-02 2.50e+03 pdb=" C24 Q6B A 501 " -0.070 2.00e-02 2.50e+03 pdb=" C32 Q6B A 501 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C19 Q6B A 501 " 0.059 2.00e-02 2.50e+03 6.07e-02 3.69e+01 pdb=" C20 Q6B A 501 " -0.052 2.00e-02 2.50e+03 pdb=" C21 Q6B A 501 " -0.069 2.00e-02 2.50e+03 pdb=" C22 Q6B A 501 " 0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C15 Q6B A 501 " -0.052 2.00e-02 2.50e+03 5.37e-02 3.60e+01 pdb=" C16 Q6B A 501 " 0.033 2.00e-02 2.50e+03 pdb=" C17 Q6B A 501 " 0.083 2.00e-02 2.50e+03 pdb=" C18 Q6B A 501 " -0.062 2.00e-02 2.50e+03 pdb=" C34 Q6B A 501 " -0.003 2.00e-02 2.50e+03 ... (remaining 715 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 995 2.79 - 3.32: 4343 3.32 - 3.85: 7299 3.85 - 4.37: 7946 4.37 - 4.90: 14498 Nonbonded interactions: 35081 Sorted by model distance: nonbonded pdb=" OE1 GLN B 13 " pdb=" NZ LYS B 16 " model vdw 2.266 2.520 nonbonded pdb=" OG SER A 287 " pdb=" O30 Q6B A 501 " model vdw 2.294 2.440 nonbonded pdb=" O TYR A 131 " pdb=" OG1 THR A 134 " model vdw 2.307 2.440 nonbonded pdb=" O01 Q6B A 501 " pdb=" O HOH A 601 " model vdw 2.313 2.440 nonbonded pdb=" O PRO A 17 " pdb=" NZ LYS A 117 " model vdw 2.315 2.520 ... (remaining 35076 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=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: 0.850 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: 3.630 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 16.750 Find NCS groups from input model: 0.140 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: 0.010 Load rotamer database and sin/cos tables:12.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 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 : 0.007 0.271 4335 Z= 0.508 Angle : 1.434 42.593 5869 Z= 0.515 Chirality : 0.040 0.200 699 Planarity : 0.005 0.062 718 Dihedral : 15.011 126.225 1562 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.22 % Allowed : 0.22 % Favored : 99.56 % 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: 2.41 (0.37), residues: 532 helix: 2.60 (0.26), residues: 376 sheet: -2.47 (1.39), residues: 14 loop : -0.79 (0.53), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 64 HIS 0.001 0.000 HIS A 360 PHE 0.029 0.001 PHE A 312 TYR 0.023 0.001 TYR A 302 ARG 0.007 0.001 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 59 time to evaluate : 0.560 Fit side-chains REVERT: B 24 ARG cc_start: 0.7996 (mmm-85) cc_final: 0.7375 (mtp180) REVERT: B 30 ARG cc_start: 0.7733 (mtm110) cc_final: 0.6118 (mmp-170) REVERT: A 133 MET cc_start: 0.8100 (mmt) cc_final: 0.7842 (mmt) REVERT: A 273 ARG cc_start: 0.6805 (mtt180) cc_final: 0.6574 (mtp180) outliers start: 1 outliers final: 0 residues processed: 60 average time/residue: 1.2690 time to fit residues: 78.9040 Evaluate side-chains 47 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 0.2980 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 42 optimal weight: 10.0000 chunk 16 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 GLN ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.0915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4335 Z= 0.219 Angle : 0.911 21.484 5869 Z= 0.353 Chirality : 0.040 0.178 699 Planarity : 0.003 0.031 718 Dihedral : 13.793 120.927 598 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.99 % Allowed : 7.28 % Favored : 90.73 % 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: 2.45 (0.37), residues: 532 helix: 2.52 (0.26), residues: 383 sheet: -2.88 (1.23), residues: 12 loop : -0.61 (0.53), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 64 HIS 0.004 0.001 HIS A 360 PHE 0.008 0.001 PHE A 156 TYR 0.012 0.001 TYR A 263 ARG 0.004 0.000 ARG A 236 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 51 time to evaluate : 0.487 Fit side-chains REVERT: B 24 ARG cc_start: 0.8064 (mmm-85) cc_final: 0.7392 (mtm180) REVERT: B 30 ARG cc_start: 0.7490 (mtm110) cc_final: 0.6268 (mmp-170) REVERT: A 133 MET cc_start: 0.8076 (mmt) cc_final: 0.7788 (mmt) REVERT: A 139 ASP cc_start: 0.8045 (t70) cc_final: 0.7845 (t70) REVERT: A 228 ARG cc_start: 0.7381 (tpp80) cc_final: 0.6983 (tpt90) REVERT: A 307 MET cc_start: 0.7887 (OUTLIER) cc_final: 0.7295 (mtt) outliers start: 9 outliers final: 2 residues processed: 54 average time/residue: 1.3076 time to fit residues: 73.4906 Evaluate side-chains 50 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 47 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 307 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 13 optimal weight: 0.0040 chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 48 optimal weight: 0.0970 chunk 16 optimal weight: 0.4980 chunk 39 optimal weight: 2.9990 overall best weight: 0.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.0974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4335 Z= 0.165 Angle : 0.880 20.420 5869 Z= 0.338 Chirality : 0.038 0.133 699 Planarity : 0.003 0.031 718 Dihedral : 13.378 114.719 598 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.21 % Allowed : 7.51 % Favored : 90.29 % 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: 2.62 (0.37), residues: 532 helix: 2.66 (0.26), residues: 383 sheet: -2.92 (1.15), residues: 12 loop : -0.56 (0.53), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 64 HIS 0.002 0.001 HIS A 360 PHE 0.015 0.001 PHE A 12 TYR 0.006 0.001 TYR A 263 ARG 0.005 0.000 ARG A 268 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 45 time to evaluate : 0.503 Fit side-chains REVERT: B 24 ARG cc_start: 0.8092 (mmm-85) cc_final: 0.7499 (mtm180) REVERT: B 30 ARG cc_start: 0.7515 (mtm110) cc_final: 0.6271 (mmp-170) REVERT: A 12 PHE cc_start: 0.8127 (m-80) cc_final: 0.7920 (m-80) REVERT: A 139 ASP cc_start: 0.8081 (t70) cc_final: 0.7841 (t0) REVERT: A 228 ARG cc_start: 0.7383 (tpp80) cc_final: 0.6980 (tpt90) REVERT: A 307 MET cc_start: 0.7870 (OUTLIER) cc_final: 0.7298 (mtt) outliers start: 10 outliers final: 5 residues processed: 49 average time/residue: 1.3238 time to fit residues: 67.3735 Evaluate side-chains 52 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 46 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 307 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 5 optimal weight: 0.0000 chunk 23 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 49 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.1152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4335 Z= 0.192 Angle : 0.867 20.275 5869 Z= 0.334 Chirality : 0.038 0.135 699 Planarity : 0.003 0.031 718 Dihedral : 13.152 116.804 598 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.77 % Allowed : 9.71 % Favored : 88.52 % 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: 2.63 (0.37), residues: 532 helix: 2.66 (0.26), residues: 383 sheet: -2.80 (1.12), residues: 12 loop : -0.53 (0.53), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 64 HIS 0.002 0.001 HIS A 360 PHE 0.008 0.001 PHE A 156 TYR 0.008 0.001 TYR A 336 ARG 0.003 0.000 ARG A 268 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 46 time to evaluate : 0.493 Fit side-chains REVERT: B 24 ARG cc_start: 0.8081 (mmm-85) cc_final: 0.7537 (mtm180) REVERT: B 30 ARG cc_start: 0.7535 (mtm110) cc_final: 0.6303 (mmp-170) REVERT: A 12 PHE cc_start: 0.8133 (m-80) cc_final: 0.7911 (m-80) REVERT: A 15 ILE cc_start: 0.8200 (OUTLIER) cc_final: 0.7824 (mp) REVERT: A 133 MET cc_start: 0.8121 (mmt) cc_final: 0.7872 (mmt) REVERT: A 139 ASP cc_start: 0.8096 (t70) cc_final: 0.7819 (t0) REVERT: A 228 ARG cc_start: 0.7386 (tpp80) cc_final: 0.6991 (tpt90) REVERT: A 307 MET cc_start: 0.7911 (OUTLIER) cc_final: 0.7309 (mtt) outliers start: 8 outliers final: 5 residues processed: 49 average time/residue: 1.3379 time to fit residues: 68.1192 Evaluate side-chains 51 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 44 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 307 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 4335 Z= 0.351 Angle : 0.909 20.358 5869 Z= 0.364 Chirality : 0.041 0.143 699 Planarity : 0.003 0.031 718 Dihedral : 13.521 124.645 598 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.21 % Allowed : 9.71 % Favored : 88.08 % 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: 2.22 (0.36), residues: 532 helix: 2.30 (0.26), residues: 388 sheet: -3.03 (1.09), residues: 12 loop : -0.62 (0.54), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 34 HIS 0.003 0.001 HIS B 58 PHE 0.011 0.002 PHE A 261 TYR 0.008 0.001 TYR A 263 ARG 0.006 0.001 ARG A 236 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 46 time to evaluate : 0.445 Fit side-chains REVERT: B 24 ARG cc_start: 0.7971 (mmm-85) cc_final: 0.7372 (mtm180) REVERT: B 30 ARG cc_start: 0.7772 (mtm110) cc_final: 0.6210 (mmp-170) REVERT: A 12 PHE cc_start: 0.8222 (m-80) cc_final: 0.7999 (m-80) REVERT: A 15 ILE cc_start: 0.8115 (OUTLIER) cc_final: 0.7646 (mp) REVERT: A 133 MET cc_start: 0.8120 (mmt) cc_final: 0.7849 (mmt) REVERT: A 139 ASP cc_start: 0.8216 (t70) cc_final: 0.7978 (t0) REVERT: A 228 ARG cc_start: 0.7454 (tpp80) cc_final: 0.7098 (tpt90) REVERT: A 307 MET cc_start: 0.8007 (OUTLIER) cc_final: 0.7407 (mtt) outliers start: 10 outliers final: 3 residues processed: 51 average time/residue: 1.2099 time to fit residues: 64.1830 Evaluate side-chains 48 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 43 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 307 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 0.0370 chunk 30 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 17 optimal weight: 0.0980 chunk 27 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4335 Z= 0.172 Angle : 0.850 19.958 5869 Z= 0.329 Chirality : 0.038 0.130 699 Planarity : 0.003 0.030 718 Dihedral : 13.256 124.007 598 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.21 % Allowed : 9.93 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.54 (0.37), residues: 532 helix: 2.56 (0.26), residues: 388 sheet: -2.92 (1.07), residues: 12 loop : -0.59 (0.53), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 64 HIS 0.001 0.000 HIS B 58 PHE 0.009 0.001 PHE A 156 TYR 0.006 0.001 TYR A 455 ARG 0.005 0.000 ARG A 268 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 44 time to evaluate : 0.505 Fit side-chains REVERT: B 24 ARG cc_start: 0.8045 (mmm-85) cc_final: 0.7536 (mtm180) REVERT: B 30 ARG cc_start: 0.7697 (mtm110) cc_final: 0.6228 (mmp-170) REVERT: A 12 PHE cc_start: 0.8193 (m-80) cc_final: 0.7971 (m-80) REVERT: A 15 ILE cc_start: 0.8138 (OUTLIER) cc_final: 0.7679 (mp) REVERT: A 139 ASP cc_start: 0.8172 (t70) cc_final: 0.7961 (t0) REVERT: A 228 ARG cc_start: 0.7433 (tpp80) cc_final: 0.7080 (tpt90) REVERT: A 307 MET cc_start: 0.7977 (OUTLIER) cc_final: 0.7400 (mtt) outliers start: 10 outliers final: 4 residues processed: 50 average time/residue: 1.3351 time to fit residues: 69.3498 Evaluate side-chains 48 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 42 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 307 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4335 Z= 0.230 Angle : 0.863 20.029 5869 Z= 0.338 Chirality : 0.039 0.136 699 Planarity : 0.003 0.031 718 Dihedral : 13.279 125.086 598 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.77 % Allowed : 11.04 % Favored : 87.20 % 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: 2.47 (0.36), residues: 532 helix: 2.50 (0.26), residues: 388 sheet: -2.97 (1.05), residues: 12 loop : -0.58 (0.53), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 64 HIS 0.002 0.001 HIS B 58 PHE 0.008 0.001 PHE B 49 TYR 0.007 0.001 TYR A 336 ARG 0.005 0.000 ARG A 268 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 45 time to evaluate : 0.513 Fit side-chains REVERT: B 24 ARG cc_start: 0.8003 (mmm-85) cc_final: 0.7471 (mtm180) REVERT: B 30 ARG cc_start: 0.7775 (mtm110) cc_final: 0.6280 (mmp-170) REVERT: A 12 PHE cc_start: 0.8237 (m-80) cc_final: 0.8001 (m-80) REVERT: A 15 ILE cc_start: 0.8192 (OUTLIER) cc_final: 0.7835 (mp) REVERT: A 139 ASP cc_start: 0.8194 (t70) cc_final: 0.7970 (t0) REVERT: A 228 ARG cc_start: 0.7457 (tpp80) cc_final: 0.7110 (tpt90) REVERT: A 243 MET cc_start: 0.7561 (OUTLIER) cc_final: 0.7338 (tpp) REVERT: A 307 MET cc_start: 0.7975 (OUTLIER) cc_final: 0.7394 (mtt) outliers start: 8 outliers final: 4 residues processed: 49 average time/residue: 1.3201 time to fit residues: 67.1983 Evaluate side-chains 51 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 44 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 307 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4335 Z= 0.256 Angle : 0.870 19.943 5869 Z= 0.343 Chirality : 0.039 0.135 699 Planarity : 0.003 0.031 718 Dihedral : 13.347 126.213 598 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.77 % Allowed : 11.48 % Favored : 86.75 % 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: 2.40 (0.36), residues: 532 helix: 2.44 (0.26), residues: 388 sheet: -3.09 (1.01), residues: 12 loop : -0.55 (0.53), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 64 HIS 0.002 0.001 HIS B 58 PHE 0.009 0.001 PHE B 49 TYR 0.009 0.001 TYR A 302 ARG 0.006 0.000 ARG A 268 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 46 time to evaluate : 0.547 Fit side-chains REVERT: B 24 ARG cc_start: 0.8035 (mmm-85) cc_final: 0.7380 (mtm180) REVERT: B 30 ARG cc_start: 0.7884 (mtm110) cc_final: 0.6392 (mmp-170) REVERT: A 12 PHE cc_start: 0.8289 (m-80) cc_final: 0.8061 (m-80) REVERT: A 15 ILE cc_start: 0.8128 (OUTLIER) cc_final: 0.7683 (mp) REVERT: A 133 MET cc_start: 0.8157 (mmt) cc_final: 0.7950 (mmt) REVERT: A 139 ASP cc_start: 0.8207 (t70) cc_final: 0.7985 (t0) REVERT: A 228 ARG cc_start: 0.7457 (tpp80) cc_final: 0.7121 (tpt90) REVERT: A 307 MET cc_start: 0.8001 (OUTLIER) cc_final: 0.7424 (mtt) outliers start: 8 outliers final: 5 residues processed: 51 average time/residue: 1.2782 time to fit residues: 67.8178 Evaluate side-chains 51 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 44 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 400 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 42 optimal weight: 8.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 4335 Z= 0.314 Angle : 0.891 19.996 5869 Z= 0.356 Chirality : 0.041 0.138 699 Planarity : 0.003 0.030 718 Dihedral : 13.489 127.951 598 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.77 % Allowed : 11.70 % Favored : 86.53 % 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: 2.24 (0.36), residues: 532 helix: 2.32 (0.26), residues: 388 sheet: -3.11 (1.02), residues: 12 loop : -0.61 (0.52), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 34 HIS 0.003 0.001 HIS B 58 PHE 0.011 0.001 PHE B 49 TYR 0.007 0.001 TYR A 344 ARG 0.005 0.001 ARG A 268 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 45 time to evaluate : 0.531 Fit side-chains REVERT: B 24 ARG cc_start: 0.7993 (mmm-85) cc_final: 0.7386 (mtm180) REVERT: B 30 ARG cc_start: 0.7958 (mtm110) cc_final: 0.6424 (mmp-170) REVERT: A 12 PHE cc_start: 0.8314 (m-80) cc_final: 0.8088 (m-80) REVERT: A 15 ILE cc_start: 0.8118 (OUTLIER) cc_final: 0.7659 (mp) REVERT: A 68 ILE cc_start: 0.8175 (OUTLIER) cc_final: 0.7815 (pt) REVERT: A 133 MET cc_start: 0.8210 (mmt) cc_final: 0.8000 (mmt) REVERT: A 139 ASP cc_start: 0.8189 (t70) cc_final: 0.7984 (t0) REVERT: A 228 ARG cc_start: 0.7428 (tpp80) cc_final: 0.7115 (tpt90) REVERT: A 307 MET cc_start: 0.8028 (OUTLIER) cc_final: 0.7454 (mtt) outliers start: 8 outliers final: 3 residues processed: 50 average time/residue: 1.2815 time to fit residues: 66.6213 Evaluate side-chains 50 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 44 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 400 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 39 optimal weight: 0.0870 chunk 6 optimal weight: 0.0370 chunk 11 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 17 optimal weight: 0.3980 overall best weight: 0.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4335 Z= 0.177 Angle : 0.854 19.673 5869 Z= 0.332 Chirality : 0.038 0.132 699 Planarity : 0.003 0.030 718 Dihedral : 13.247 126.563 598 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.55 % Allowed : 11.92 % Favored : 86.53 % 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: 2.54 (0.36), residues: 532 helix: 2.55 (0.26), residues: 388 sheet: -2.88 (1.04), residues: 12 loop : -0.59 (0.52), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 64 HIS 0.001 0.000 HIS B 58 PHE 0.009 0.001 PHE A 156 TYR 0.007 0.001 TYR A 302 ARG 0.006 0.000 ARG A 268 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 45 time to evaluate : 0.520 Fit side-chains REVERT: B 24 ARG cc_start: 0.8003 (mmm-85) cc_final: 0.7423 (mtm180) REVERT: B 30 ARG cc_start: 0.7880 (mtm110) cc_final: 0.6448 (mmp-170) REVERT: A 12 PHE cc_start: 0.8307 (m-80) cc_final: 0.8086 (m-80) REVERT: A 15 ILE cc_start: 0.8196 (OUTLIER) cc_final: 0.7844 (mp) REVERT: A 68 ILE cc_start: 0.8273 (OUTLIER) cc_final: 0.7800 (pt) REVERT: A 139 ASP cc_start: 0.8206 (t70) cc_final: 0.7988 (t0) REVERT: A 228 ARG cc_start: 0.7416 (tpp80) cc_final: 0.7101 (tpt90) REVERT: A 243 MET cc_start: 0.7629 (OUTLIER) cc_final: 0.7329 (tpp) REVERT: A 307 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.7423 (mtt) outliers start: 7 outliers final: 2 residues processed: 49 average time/residue: 1.3823 time to fit residues: 70.4063 Evaluate side-chains 50 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 44 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 307 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 30 optimal weight: 0.4980 chunk 49 optimal weight: 0.5980 chunk 28 optimal weight: 0.0770 chunk 36 optimal weight: 0.2980 chunk 1 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** 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 = 0.3625 r_free = 0.3625 target = 0.142693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.112757 restraints weight = 4738.297| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.86 r_work: 0.3180 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4335 Z= 0.180 Angle : 0.849 19.675 5869 Z= 0.331 Chirality : 0.038 0.133 699 Planarity : 0.003 0.030 718 Dihedral : 13.147 126.683 598 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.32 % Allowed : 12.14 % Favored : 86.53 % 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: 2.58 (0.36), residues: 532 helix: 2.60 (0.26), residues: 388 sheet: -2.80 (1.08), residues: 12 loop : -0.62 (0.51), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 64 HIS 0.001 0.000 HIS B 58 PHE 0.010 0.001 PHE A 312 TYR 0.010 0.001 TYR A 302 ARG 0.006 0.000 ARG A 268 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1850.52 seconds wall clock time: 33 minutes 48.15 seconds (2028.15 seconds total)