Starting phenix.real_space_refine on Thu Dec 7 20:21:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8do0_27586/12_2023/8do0_27586_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8do0_27586/12_2023/8do0_27586.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8do0_27586/12_2023/8do0_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_27586/12_2023/8do0_27586_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8do0_27586/12_2023/8do0_27586_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8do0_27586/12_2023/8do0_27586.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8do0_27586/12_2023/8do0_27586.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8do0_27586/12_2023/8do0_27586_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8do0_27586/12_2023/8do0_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-1.21rc1-5172/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: 2.90, per 1000 atoms: 0.68 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: 1.83 Conformation dependent library (CDL) restraints added in 817.8 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: 0.81 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: 1.11 Time building geometry restraints manager: 1.94 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: 0.610 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: 3.640 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 16.900 Find NCS groups from input model: 0.120 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:12.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.750 ------------------------------------------------------------------------------- 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 : 0.483 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 60 average time/residue: 1.2688 time to fit residues: 79.0129 Evaluate side-chains 46 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.506 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7063 ------------------------------------------------------------------------------- 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: 0.9980 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 42 optimal weight: 10.0000 chunk 16 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.7702 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4335 Z= 0.242 Angle : 0.916 20.833 5869 Z= 0.356 Chirality : 0.040 0.163 699 Planarity : 0.003 0.032 718 Dihedral : 13.862 120.844 598 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.99 % Allowed : 7.95 % Favored : 90.07 % 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 (0.37), residues: 532 helix: 2.48 (0.26), residues: 383 sheet: -2.87 (1.23), residues: 12 loop : -0.62 (0.54), 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 B 52 TYR 0.007 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 58 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 49 time to evaluate : 0.506 Fit side-chains outliers start: 9 outliers final: 3 residues processed: 52 average time/residue: 1.2923 time to fit residues: 69.9421 Evaluate side-chains 51 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 48 time to evaluate : 0.404 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 1 residues processed: 2 average time/residue: 0.6701 time to fit residues: 2.1168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 0.9990 chunk 15 optimal weight: 0.2980 chunk 40 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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: 0.7696 moved from start: 0.1238 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= 0.196 Angle : 0.892 20.338 5869 Z= 0.344 Chirality : 0.039 0.135 699 Planarity : 0.003 0.031 718 Dihedral : 13.475 115.249 598 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.55 % Allowed : 9.49 % Favored : 88.96 % 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: 2.49 (0.37), residues: 532 helix: 2.56 (0.26), residues: 383 sheet: -2.88 (1.16), residues: 12 loop : -0.62 (0.53), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 64 HIS 0.003 0.001 HIS A 360 PHE 0.008 0.001 PHE A 156 TYR 0.006 0.001 TYR A 455 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 53 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 46 time to evaluate : 0.447 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 49 average time/residue: 1.3939 time to fit residues: 70.8694 Evaluate side-chains 49 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 45 time to evaluate : 0.510 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 0.0775 time to fit residues: 0.9011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 0.5980 chunk 36 optimal weight: 0.3980 chunk 25 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4335 Z= 0.221 Angle : 0.885 19.994 5869 Z= 0.345 Chirality : 0.039 0.136 699 Planarity : 0.003 0.031 718 Dihedral : 13.194 118.086 598 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.21 % Allowed : 10.82 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.48 (0.37), residues: 532 helix: 2.56 (0.26), residues: 383 sheet: -2.86 (1.15), residues: 12 loop : -0.63 (0.53), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 34 HIS 0.002 0.001 HIS A 360 PHE 0.015 0.001 PHE A 12 TYR 0.008 0.001 TYR A 336 ARG 0.005 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 56 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 46 time to evaluate : 0.496 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 50 average time/residue: 1.3658 time to fit residues: 70.9718 Evaluate side-chains 47 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 43 time to evaluate : 0.516 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 0.0712 time to fit residues: 0.8950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 36 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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: 0.7752 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4335 Z= 0.290 Angle : 0.897 19.975 5869 Z= 0.355 Chirality : 0.040 0.138 699 Planarity : 0.003 0.031 718 Dihedral : 13.422 124.368 598 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.55 % Allowed : 11.26 % 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: 2.28 (0.36), residues: 532 helix: 2.36 (0.26), residues: 384 sheet: -3.04 (1.07), residues: 12 loop : -0.59 (0.53), residues: 136 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 0.010 0.001 PHE B 49 TYR 0.007 0.001 TYR A 343 ARG 0.005 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 52 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 45 time to evaluate : 0.531 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 49 average time/residue: 1.3766 time to fit residues: 69.9922 Evaluate side-chains 46 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 43 time to evaluate : 0.495 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.6874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 0.0470 chunk 30 optimal weight: 6.9990 chunk 12 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 50 optimal weight: 0.0570 chunk 5 optimal weight: 0.9990 overall best weight: 0.3996 ------------------------------------------------------------------------------- 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: 0.7707 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4335 Z= 0.168 Angle : 0.861 19.836 5869 Z= 0.334 Chirality : 0.038 0.132 699 Planarity : 0.003 0.030 718 Dihedral : 13.250 124.328 598 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.55 % Allowed : 11.70 % 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: 2.52 (0.37), residues: 532 helix: 2.59 (0.26), residues: 383 sheet: -2.91 (1.07), residues: 12 loop : -0.63 (0.52), residues: 137 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 0.014 0.001 PHE A 12 TYR 0.007 0.001 TYR A 336 ARG 0.006 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 52 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 45 time to evaluate : 0.495 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 49 average time/residue: 1.3449 time to fit residues: 68.4194 Evaluate side-chains 47 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 42 time to evaluate : 0.536 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 2 average time/residue: 0.5990 time to fit residues: 1.9537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 43 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- 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: 0.7738 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4335 Z= 0.257 Angle : 0.884 19.823 5869 Z= 0.350 Chirality : 0.039 0.137 699 Planarity : 0.003 0.031 718 Dihedral : 13.346 125.973 598 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.88 % Allowed : 13.02 % Favored : 86.09 % 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: 2.46 (0.26), residues: 384 sheet: -3.02 (1.07), residues: 12 loop : -0.57 (0.52), residues: 136 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 0.006 0.001 TYR A 455 ARG 0.005 0.001 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 48 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 44 time to evaluate : 0.551 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 48 average time/residue: 1.3387 time to fit residues: 66.7478 Evaluate side-chains 47 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 43 time to evaluate : 0.496 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 0.6783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.7732 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4335 Z= 0.232 Angle : 0.875 19.760 5869 Z= 0.344 Chirality : 0.039 0.134 699 Planarity : 0.003 0.030 718 Dihedral : 13.307 126.430 598 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.32 % Allowed : 13.25 % Favored : 85.43 % 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: 2.43 (0.36), residues: 532 helix: 2.53 (0.26), residues: 383 sheet: -3.01 (1.09), residues: 12 loop : -0.66 (0.52), residues: 137 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 0.017 0.001 PHE A 12 TYR 0.007 0.001 TYR A 302 ARG 0.006 0.001 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 51 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 45 time to evaluate : 0.455 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 50 average time/residue: 1.3257 time to fit residues: 68.7607 Evaluate side-chains 47 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 44 time to evaluate : 0.451 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.6730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 31 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 42 optimal weight: 7.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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: 0.7742 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4335 Z= 0.266 Angle : 0.889 19.778 5869 Z= 0.351 Chirality : 0.040 0.136 699 Planarity : 0.003 0.031 718 Dihedral : 13.352 126.811 598 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.88 % Allowed : 13.02 % Favored : 86.09 % 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: 2.35 (0.36), residues: 532 helix: 2.47 (0.26), residues: 383 sheet: -2.97 (1.14), residues: 12 loop : -0.69 (0.51), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 34 HIS 0.002 0.001 HIS B 58 PHE 0.009 0.001 PHE B 49 TYR 0.007 0.001 TYR A 137 ARG 0.007 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 49 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 45 time to evaluate : 0.532 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 49 average time/residue: 1.3254 time to fit residues: 67.4699 Evaluate side-chains 47 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 44 time to evaluate : 0.490 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.6856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.4980 chunk 26 optimal weight: 2.9990 chunk 34 optimal weight: 0.0070 chunk 45 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 39 optimal weight: 0.0370 chunk 6 optimal weight: 0.0030 chunk 11 optimal weight: 0.5980 chunk 42 optimal weight: 6.9990 chunk 17 optimal weight: 0.5980 overall best weight: 0.2286 ------------------------------------------------------------------------------- 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: 0.7681 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 4335 Z= 0.159 Angle : 0.857 19.615 5869 Z= 0.332 Chirality : 0.038 0.129 699 Planarity : 0.003 0.030 718 Dihedral : 13.089 125.962 598 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.88 % Allowed : 13.02 % Favored : 86.09 % 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: 2.70 (0.37), residues: 532 helix: 2.71 (0.26), residues: 383 sheet: -2.72 (1.15), residues: 12 loop : -0.55 (0.51), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 64 HIS 0.001 0.000 HIS B 58 PHE 0.014 0.001 PHE A 12 TYR 0.009 0.001 TYR A 302 ARG 0.007 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 48 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 44 time to evaluate : 0.512 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 47 average time/residue: 1.3144 time to fit residues: 64.2156 Evaluate side-chains 46 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 43 time to evaluate : 0.496 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.6933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 7 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 chunk 28 optimal weight: 0.4980 chunk 36 optimal weight: 0.4980 chunk 1 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3629 r_free = 0.3629 target = 0.142641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.112392 restraints weight = 4719.910| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.87 r_work: 0.3183 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4335 Z= 0.211 Angle : 0.869 19.685 5869 Z= 0.340 Chirality : 0.039 0.134 699 Planarity : 0.003 0.030 718 Dihedral : 13.128 127.205 598 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.88 % Allowed : 13.91 % 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: 2.61 (0.36), residues: 532 helix: 2.64 (0.26), residues: 383 sheet: -2.82 (1.17), residues: 12 loop : -0.53 (0.51), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 34 HIS 0.002 0.001 HIS B 58 PHE 0.009 0.001 PHE A 312 TYR 0.008 0.001 TYR A 302 ARG 0.007 0.001 ARG A 268 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1862.10 seconds wall clock time: 33 minutes 52.28 seconds (2032.28 seconds total)