Starting phenix.real_space_refine on Sun Mar 10 19:03:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgg_22326/03_2024/7jgg_22326.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgg_22326/03_2024/7jgg_22326.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgg_22326/03_2024/7jgg_22326.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgg_22326/03_2024/7jgg_22326.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgg_22326/03_2024/7jgg_22326.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgg_22326/03_2024/7jgg_22326.pdb" } resolution = 4.88 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 27 5.16 5 C 2643 2.51 5 N 713 2.21 5 O 799 1.98 5 H 28 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 2018": "OD1" <-> "OD2" Residue "A ASP 2020": "OD1" <-> "OD2" Residue "A ASP 2023": "OD1" <-> "OD2" Residue "A PHE 2042": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2058": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2060": "OE1" <-> "OE2" Residue "A GLU 2069": "OE1" <-> "OE2" Residue "A PHE 2072": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2079": "OE1" <-> "OE2" Residue "A TYR 2095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2120": "OD1" <-> "OD2" Residue "A GLU 2126": "OE1" <-> "OE2" Residue "A GLU 2221": "OE1" <-> "OE2" Residue "A TYR 2243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2354": "OD1" <-> "OD2" Residue "A PHE 2376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2381": "OE1" <-> "OE2" Residue "A PHE 2397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2430": "OD1" <-> "OD2" Residue "A GLU 2461": "OE1" <-> "OE2" Residue "A TYR 2472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2503": "OD1" <-> "OD2" Residue "A GLU 2517": "OE1" <-> "OE2" Residue "A PHE 2519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2577": "OD1" <-> "OD2" Residue "A GLU 2582": "OE1" <-> "OE2" Residue "A GLU 2592": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 4210 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 4210 Classifications: {'peptide': 506} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 491} Chain breaks: 7 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 2.21, per 1000 atoms: 0.52 Number of scatterers: 4210 At special positions: 0 Unit cell: (75.118, 131.192, 93.104, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 27 16.00 O 799 8.00 N 713 7.00 C 2643 6.00 H 28 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A2202 " - pdb=" SG CYS A2218 " distance=2.03 Simple disulfide: pdb=" SG CYS A2334 " - pdb=" SG CYS A2480 " distance=2.03 Simple disulfide: pdb=" SG CYS A2520 " - pdb=" SG CYS A2604 " distance=2.03 Simple disulfide: pdb=" SG CYS A2534 " - pdb=" SG CYS A2551 " distance=2.03 Simple disulfide: pdb=" SG CYS A2598 " - pdb=" SG CYS A2602 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.67 Conformation dependent library (CDL) restraints added in 643.4 milliseconds 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 962 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 0 sheets defined 70.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 2017 through 2026 Proline residue: A2024 - end of helix Processing helix chain 'A' and resid 2034 through 2039 removed outlier: 3.937A pdb=" N GLN A2039 " --> pdb=" O PRO A2035 " (cutoff:3.500A) Processing helix chain 'A' and resid 2054 through 2081 Processing helix chain 'A' and resid 2084 through 2102 Processing helix chain 'A' and resid 2113 through 2125 removed outlier: 3.708A pdb=" N LYS A2125 " --> pdb=" O ARG A2121 " (cutoff:3.500A) Processing helix chain 'A' and resid 2129 through 2147 removed outlier: 4.073A pdb=" N VAL A2133 " --> pdb=" O ASN A2129 " (cutoff:3.500A) Processing helix chain 'A' and resid 2174 through 2201 removed outlier: 3.585A pdb=" N LYS A2201 " --> pdb=" O TYR A2197 " (cutoff:3.500A) Processing helix chain 'A' and resid 2211 through 2214 Processing helix chain 'A' and resid 2215 through 2247 removed outlier: 3.821A pdb=" N THR A2219 " --> pdb=" O SER A2215 " (cutoff:3.500A) Processing helix chain 'A' and resid 2298 through 2303 removed outlier: 3.647A pdb=" N LYS A2302 " --> pdb=" O ASN A2298 " (cutoff:3.500A) Processing helix chain 'A' and resid 2305 through 2309 Processing helix chain 'A' and resid 2332 through 2334 No H-bonds generated for 'chain 'A' and resid 2332 through 2334' Processing helix chain 'A' and resid 2335 through 2340 Processing helix chain 'A' and resid 2369 through 2374 removed outlier: 4.100A pdb=" N ASN A2374 " --> pdb=" O PRO A2370 " (cutoff:3.500A) Processing helix chain 'A' and resid 2380 through 2382 No H-bonds generated for 'chain 'A' and resid 2380 through 2382' Processing helix chain 'A' and resid 2383 through 2390 removed outlier: 3.621A pdb=" N LYS A2388 " --> pdb=" O ILE A2384 " (cutoff:3.500A) Processing helix chain 'A' and resid 2390 through 2414 removed outlier: 3.746A pdb=" N PHE A2394 " --> pdb=" O ASP A2390 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLY A2414 " --> pdb=" O LYS A2410 " (cutoff:3.500A) Processing helix chain 'A' and resid 2416 through 2436 Processing helix chain 'A' and resid 2442 through 2453 removed outlier: 3.750A pdb=" N SER A2446 " --> pdb=" O GLU A2442 " (cutoff:3.500A) Processing helix chain 'A' and resid 2460 through 2486 Processing helix chain 'A' and resid 2506 through 2535 removed outlier: 3.537A pdb=" N PHE A2512 " --> pdb=" O PHE A2508 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N CYS A2534 " --> pdb=" O MET A2530 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN A2535 " --> pdb=" O VAL A2531 " (cutoff:3.500A) Processing helix chain 'A' and resid 2549 through 2552 Processing helix chain 'A' and resid 2553 through 2581 removed outlier: 3.883A pdb=" N ASN A2557 " --> pdb=" O GLU A2553 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR A2558 " --> pdb=" O ALA A2554 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS A2581 " --> pdb=" O ASP A2577 " (cutoff:3.500A) Processing helix chain 'A' and resid 2589 through 2597 243 hydrogen bonds defined for protein. 717 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: 1.00 Time building geometry restraints manager: 1.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.86 - 1.05: 28 1.05 - 1.24: 543 1.24 - 1.43: 1258 1.43 - 1.62: 2425 1.62 - 1.81: 38 Bond restraints: 4292 Sorted by residual: bond pdb=" CB PRO A2391 " pdb=" CG PRO A2391 " ideal model delta sigma weight residual 1.492 1.594 -0.102 5.00e-02 4.00e+02 4.20e+00 bond pdb=" CB LEU A2040 " pdb=" CG LEU A2040 " ideal model delta sigma weight residual 1.530 1.552 -0.022 2.00e-02 2.50e+03 1.20e+00 bond pdb=" CA PRO A2391 " pdb=" CB PRO A2391 " ideal model delta sigma weight residual 1.533 1.543 -0.010 1.42e-02 4.96e+03 5.25e-01 bond pdb=" N PRO A2391 " pdb=" CD PRO A2391 " ideal model delta sigma weight residual 1.473 1.463 0.010 1.40e-02 5.10e+03 4.93e-01 bond pdb=" N PRO A2034 " pdb=" CA PRO A2034 " ideal model delta sigma weight residual 1.459 1.469 -0.009 1.40e-02 5.10e+03 4.36e-01 ... (remaining 4287 not shown) Histogram of bond angle deviations from ideal: 99.07 - 106.05: 64 106.05 - 113.03: 2281 113.03 - 120.01: 1502 120.01 - 126.99: 1863 126.99 - 133.97: 51 Bond angle restraints: 5761 Sorted by residual: angle pdb=" CA PRO A2391 " pdb=" N PRO A2391 " pdb=" CD PRO A2391 " ideal model delta sigma weight residual 112.00 106.54 5.46 1.40e+00 5.10e-01 1.52e+01 angle pdb=" CB LEU A2040 " pdb=" CG LEU A2040 " pdb=" CD1 LEU A2040 " ideal model delta sigma weight residual 110.70 121.06 -10.36 3.00e+00 1.11e-01 1.19e+01 angle pdb=" C GLN A2039 " pdb=" N LEU A2040 " pdb=" CA LEU A2040 " ideal model delta sigma weight residual 121.54 127.66 -6.12 1.91e+00 2.74e-01 1.03e+01 angle pdb=" N PRO A2391 " pdb=" CD PRO A2391 " pdb=" CG PRO A2391 " ideal model delta sigma weight residual 103.20 99.07 4.13 1.50e+00 4.44e-01 7.59e+00 angle pdb=" C ARG A2038 " pdb=" N GLN A2039 " pdb=" CA GLN A2039 " ideal model delta sigma weight residual 121.54 116.46 5.08 1.91e+00 2.74e-01 7.07e+00 ... (remaining 5756 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 2380 17.95 - 35.90: 220 35.90 - 53.84: 30 53.84 - 71.79: 4 71.79 - 89.74: 4 Dihedral angle restraints: 2638 sinusoidal: 1151 harmonic: 1487 Sorted by residual: dihedral pdb=" CB CYS A2334 " pdb=" SG CYS A2334 " pdb=" SG CYS A2480 " pdb=" CB CYS A2480 " ideal model delta sinusoidal sigma weight residual -86.00 -162.76 76.76 1 1.00e+01 1.00e-02 7.40e+01 dihedral pdb=" CB CYS A2202 " pdb=" SG CYS A2202 " pdb=" SG CYS A2218 " pdb=" CB CYS A2218 " ideal model delta sinusoidal sigma weight residual -86.00 -17.19 -68.81 1 1.00e+01 1.00e-02 6.13e+01 dihedral pdb=" CA GLN A2039 " pdb=" C GLN A2039 " pdb=" N LEU A2040 " pdb=" CA LEU A2040 " ideal model delta harmonic sigma weight residual 180.00 147.28 32.72 0 5.00e+00 4.00e-02 4.28e+01 ... (remaining 2635 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 537 0.060 - 0.120: 41 0.120 - 0.180: 2 0.180 - 0.240: 0 0.240 - 0.300: 1 Chirality restraints: 581 Sorted by residual: chirality pdb=" CG LEU A2040 " pdb=" CB LEU A2040 " pdb=" CD1 LEU A2040 " pdb=" CD2 LEU A2040 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CA LEU A2040 " pdb=" N LEU A2040 " pdb=" C LEU A2040 " pdb=" CB LEU A2040 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.46e-01 chirality pdb=" CA ILE A2499 " pdb=" N ILE A2499 " pdb=" C ILE A2499 " pdb=" CB ILE A2499 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.03e-01 ... (remaining 578 not shown) Planarity restraints: 728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A2390 " 0.056 5.00e-02 4.00e+02 8.30e-02 1.10e+01 pdb=" N PRO A2391 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO A2391 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A2391 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN A2039 " 0.011 2.00e-02 2.50e+03 2.28e-02 5.19e+00 pdb=" C GLN A2039 " -0.039 2.00e-02 2.50e+03 pdb=" O GLN A2039 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU A2040 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A2515 " 0.016 2.00e-02 2.50e+03 1.03e-02 2.64e+00 pdb=" CG TRP A2515 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TRP A2515 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP A2515 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A2515 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A2515 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A2515 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A2515 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP A2515 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A2515 " -0.000 2.00e-02 2.50e+03 ... (remaining 725 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.51: 56 2.51 - 3.03: 3194 3.03 - 3.56: 5619 3.56 - 4.08: 6954 4.08 - 4.60: 10945 Nonbonded interactions: 26768 Sorted by model distance: nonbonded pdb=" O LYS A2199 " pdb=" OG SER A2203 " model vdw 1.988 2.200 nonbonded pdb=" OE2 GLU A2415 " pdb=" OH TYR A2486 " model vdw 2.077 2.200 nonbonded pdb=" OG1 THR A2521 " pdb=" NZ LYS A2522 " model vdw 2.204 2.350 nonbonded pdb=" O ILE A2100 " pdb=" NZ LYS A2113 " model vdw 2.209 2.350 nonbonded pdb=" O LYS A2216 " pdb=" OG1 THR A2219 " model vdw 2.221 2.200 ... (remaining 26763 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.75 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.700 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: 0.090 Extract box with map and model: 5.470 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 14.490 Find NCS groups from input model: 0.100 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6428 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 : 0.002 0.102 4264 Z= 0.143 Angle : 0.464 10.363 5710 Z= 0.284 Chirality : 0.034 0.300 581 Planarity : 0.004 0.083 728 Dihedral : 13.224 89.738 1650 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 54.49 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.27 % Favored : 96.53 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.39), residues: 490 helix: 2.22 (0.31), residues: 302 sheet: None (None), residues: 0 loop : -0.78 (0.44), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A2515 HIS 0.000 0.000 HIS A2506 PHE 0.017 0.001 PHE A2094 TYR 0.007 0.000 TYR A2593 ARG 0.001 0.000 ARG A2178 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2060 GLU cc_start: 0.7934 (tp30) cc_final: 0.7689 (mm-30) REVERT: A 2576 TYR cc_start: 0.7797 (t80) cc_final: 0.7540 (m-80) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.1871 time to fit residues: 8.5780 Evaluate side-chains 28 residues out of total 463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 0.9990 chunk 37 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 23 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 45 optimal weight: 9.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2459 GLN ** A2506 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6522 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4264 Z= 0.207 Angle : 0.506 6.055 5710 Z= 0.284 Chirality : 0.034 0.200 581 Planarity : 0.004 0.039 728 Dihedral : 3.631 27.247 544 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 76.48 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.69 % Favored : 95.10 % Rotamer: Outliers : 0.43 % Allowed : 4.56 % Favored : 95.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.38), residues: 490 helix: 2.47 (0.28), residues: 316 sheet: None (None), residues: 0 loop : -0.95 (0.47), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A2511 HIS 0.004 0.001 HIS A2506 PHE 0.016 0.002 PHE A2058 TYR 0.010 0.001 TYR A2076 ARG 0.005 0.001 ARG A2053 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 32 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 34 average time/residue: 0.1626 time to fit residues: 7.4867 Evaluate side-chains 27 residues out of total 463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 0.3980 chunk 14 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 chunk 36 optimal weight: 20.0000 chunk 44 optimal weight: 5.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2506 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6525 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 4264 Z= 0.143 Angle : 0.406 4.208 5710 Z= 0.233 Chirality : 0.032 0.126 581 Planarity : 0.003 0.026 728 Dihedral : 3.626 29.261 544 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 74.66 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.47 % Favored : 96.33 % Rotamer: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % 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: 2.29 (0.39), residues: 490 helix: 2.73 (0.29), residues: 314 sheet: None (None), residues: 0 loop : -0.83 (0.46), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A2511 HIS 0.002 0.001 HIS A2506 PHE 0.014 0.002 PHE A2176 TYR 0.012 0.001 TYR A2580 ARG 0.002 0.000 ARG A2038 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2060 GLU cc_start: 0.8224 (tp30) cc_final: 0.7990 (mm-30) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.1637 time to fit residues: 7.6882 Evaluate side-chains 28 residues out of total 463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 48 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 40 optimal weight: 0.4980 chunk 27 optimal weight: 8.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2473 HIS ** A2573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6544 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 4264 Z= 0.134 Angle : 0.405 4.249 5710 Z= 0.232 Chirality : 0.033 0.165 581 Planarity : 0.003 0.028 728 Dihedral : 3.678 28.901 544 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 76.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % 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: 2.09 (0.39), residues: 490 helix: 2.53 (0.29), residues: 321 sheet: None (None), residues: 0 loop : -0.97 (0.47), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A2511 HIS 0.001 0.001 HIS A2473 PHE 0.018 0.002 PHE A2094 TYR 0.012 0.001 TYR A2197 ARG 0.002 0.000 ARG A2053 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2021 MET cc_start: 0.2225 (mtt) cc_final: 0.1681 (mtt) REVERT: A 2060 GLU cc_start: 0.8385 (tp30) cc_final: 0.8005 (mm-30) REVERT: A 2249 MET cc_start: 0.7458 (mmt) cc_final: 0.7020 (mmt) REVERT: A 2426 TYR cc_start: 0.7686 (t80) cc_final: 0.7360 (t80) REVERT: A 2430 ASP cc_start: 0.9114 (t0) cc_final: 0.8750 (m-30) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.1482 time to fit residues: 7.2107 Evaluate side-chains 27 residues out of total 463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 20.0000 chunk 35 optimal weight: 0.0980 chunk 19 optimal weight: 20.0000 chunk 41 optimal weight: 8.9990 chunk 33 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 9 optimal weight: 10.0000 chunk 28 optimal weight: 0.0770 overall best weight: 2.0342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6602 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 4264 Z= 0.148 Angle : 0.422 3.852 5710 Z= 0.248 Chirality : 0.033 0.173 581 Planarity : 0.003 0.030 728 Dihedral : 3.761 29.215 544 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 81.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.38), residues: 490 helix: 2.44 (0.29), residues: 320 sheet: None (None), residues: 0 loop : -1.07 (0.46), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP A2136 HIS 0.002 0.001 HIS A2194 PHE 0.014 0.002 PHE A2176 TYR 0.009 0.001 TYR A2580 ARG 0.003 0.000 ARG A2038 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2249 MET cc_start: 0.7685 (mmt) cc_final: 0.7246 (mmt) REVERT: A 2426 TYR cc_start: 0.7707 (t80) cc_final: 0.7416 (t80) REVERT: A 2430 ASP cc_start: 0.9159 (t0) cc_final: 0.8800 (m-30) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1496 time to fit residues: 6.8972 Evaluate side-chains 27 residues out of total 463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 0.8980 chunk 48 optimal weight: 10.0000 chunk 40 optimal weight: 20.0000 chunk 22 optimal weight: 10.0000 chunk 4 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 46 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 chunk 35 optimal weight: 0.0770 overall best weight: 2.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6613 moved from start: 0.4293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4264 Z= 0.165 Angle : 0.452 4.133 5710 Z= 0.261 Chirality : 0.033 0.126 581 Planarity : 0.003 0.032 728 Dihedral : 3.872 29.483 544 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 86.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.38), residues: 490 helix: 2.19 (0.29), residues: 325 sheet: None (None), residues: 0 loop : -1.26 (0.46), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.002 TRP A2136 HIS 0.001 0.001 HIS A2506 PHE 0.015 0.002 PHE A2176 TYR 0.009 0.001 TYR A2580 ARG 0.004 0.001 ARG A2038 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2136 TRP cc_start: 0.9555 (m-90) cc_final: 0.9276 (m-90) REVERT: A 2426 TYR cc_start: 0.7954 (t80) cc_final: 0.7589 (t80) REVERT: A 2430 ASP cc_start: 0.9261 (t0) cc_final: 0.8906 (m-30) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1460 time to fit residues: 6.7855 Evaluate side-chains 25 residues out of total 463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 10.0000 chunk 40 optimal weight: 20.0000 chunk 48 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 22 optimal weight: 10.0000 chunk 19 optimal weight: 30.0000 chunk 28 optimal weight: 0.8980 chunk 14 optimal weight: 7.9990 chunk 9 optimal weight: 8.9990 chunk 32 optimal weight: 10.0000 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2054 ASN ** A2140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2506 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2524 ASN ** A2529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6678 moved from start: 0.5645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4264 Z= 0.265 Angle : 0.608 5.110 5710 Z= 0.348 Chirality : 0.039 0.154 581 Planarity : 0.004 0.041 728 Dihedral : 4.503 32.092 544 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 109.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.37), residues: 490 helix: 1.40 (0.28), residues: 321 sheet: None (None), residues: 0 loop : -1.51 (0.45), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A2136 HIS 0.005 0.002 HIS A2473 PHE 0.025 0.004 PHE A2176 TYR 0.017 0.002 TYR A2197 ARG 0.009 0.001 ARG A2038 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2021 MET cc_start: 0.1929 (mtt) cc_final: 0.1709 (mtt) REVERT: A 2136 TRP cc_start: 0.9375 (m-90) cc_final: 0.9031 (m-90) REVERT: A 2148 MET cc_start: 0.0673 (mmp) cc_final: 0.0390 (mmp) REVERT: A 2426 TYR cc_start: 0.8481 (t80) cc_final: 0.8089 (t80) REVERT: A 2430 ASP cc_start: 0.9384 (t0) cc_final: 0.9071 (m-30) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.1498 time to fit residues: 6.7134 Evaluate side-chains 23 residues out of total 463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 27 optimal weight: 10.0000 chunk 19 optimal weight: 20.0000 chunk 35 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6638 moved from start: 0.5708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4264 Z= 0.170 Angle : 0.474 5.179 5710 Z= 0.270 Chirality : 0.035 0.139 581 Planarity : 0.004 0.043 728 Dihedral : 4.327 32.265 544 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 94.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.38), residues: 490 helix: 1.66 (0.28), residues: 322 sheet: None (None), residues: 0 loop : -1.39 (0.46), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A2136 HIS 0.002 0.001 HIS A2506 PHE 0.022 0.003 PHE A2512 TYR 0.013 0.001 TYR A2580 ARG 0.005 0.001 ARG A2038 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2136 TRP cc_start: 0.9303 (m-90) cc_final: 0.8945 (m-90) REVERT: A 2249 MET cc_start: 0.8407 (mmt) cc_final: 0.8110 (mmt) REVERT: A 2426 TYR cc_start: 0.8313 (t80) cc_final: 0.8000 (t80) REVERT: A 2430 ASP cc_start: 0.9383 (t0) cc_final: 0.9056 (m-30) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.1701 time to fit residues: 7.4120 Evaluate side-chains 22 residues out of total 463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 30.0000 chunk 42 optimal weight: 10.0000 chunk 44 optimal weight: 0.0020 chunk 29 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 28 optimal weight: 8.9990 chunk 22 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 39 optimal weight: 20.0000 overall best weight: 1.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2506 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6625 moved from start: 0.5843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 4264 Z= 0.132 Angle : 0.430 4.299 5710 Z= 0.248 Chirality : 0.034 0.119 581 Planarity : 0.003 0.040 728 Dihedral : 4.104 31.064 544 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 89.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.38), residues: 490 helix: 1.86 (0.29), residues: 321 sheet: None (None), residues: 0 loop : -1.21 (0.48), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A2136 HIS 0.003 0.001 HIS A2194 PHE 0.016 0.002 PHE A2512 TYR 0.024 0.001 TYR A2197 ARG 0.004 0.000 ARG A2038 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2021 MET cc_start: 0.1908 (mtt) cc_final: 0.1700 (mtt) REVERT: A 2136 TRP cc_start: 0.9266 (m-90) cc_final: 0.8888 (m-90) REVERT: A 2426 TYR cc_start: 0.8224 (t80) cc_final: 0.7883 (t80) REVERT: A 2430 ASP cc_start: 0.9398 (t0) cc_final: 0.9068 (m-30) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.1590 time to fit residues: 7.0092 Evaluate side-chains 22 residues out of total 463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 1.9990 chunk 30 optimal weight: 0.0980 chunk 24 optimal weight: 0.0570 chunk 31 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 16 optimal weight: 7.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6616 moved from start: 0.5748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 4264 Z= 0.104 Angle : 0.402 4.103 5710 Z= 0.229 Chirality : 0.033 0.120 581 Planarity : 0.003 0.041 728 Dihedral : 3.881 29.077 544 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 76.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.39), residues: 490 helix: 2.12 (0.29), residues: 321 sheet: None (None), residues: 0 loop : -0.97 (0.50), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A2136 HIS 0.001 0.000 HIS A2484 PHE 0.015 0.002 PHE A2094 TYR 0.015 0.001 TYR A2197 ARG 0.002 0.000 ARG A2038 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2136 TRP cc_start: 0.9262 (m-90) cc_final: 0.8993 (m-90) REVERT: A 2426 TYR cc_start: 0.8173 (t80) cc_final: 0.7810 (t80) REVERT: A 2430 ASP cc_start: 0.9378 (t0) cc_final: 0.9035 (m-30) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.1669 time to fit residues: 7.7565 Evaluate side-chains 24 residues out of total 463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 2 optimal weight: 0.0030 chunk 28 optimal weight: 0.4980 chunk 45 optimal weight: 0.8980 chunk 26 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 30 optimal weight: 0.1980 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2307 GLN ** A2341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2470 ASN ** A2573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.059576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.049519 restraints weight = 62486.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.049245 restraints weight = 60830.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.049429 restraints weight = 63043.950| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3367 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3367 r_free = 0.3367 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3367 r_free = 0.3367 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3367 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.5775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4264 Z= 0.099 Angle : 0.383 3.929 5710 Z= 0.220 Chirality : 0.033 0.118 581 Planarity : 0.003 0.041 728 Dihedral : 3.671 27.129 544 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 75.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.40), residues: 490 helix: 2.32 (0.29), residues: 323 sheet: None (None), residues: 0 loop : -0.87 (0.51), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A2136 HIS 0.002 0.001 HIS A2194 PHE 0.018 0.002 PHE A2094 TYR 0.006 0.001 TYR A2580 ARG 0.002 0.000 ARG A2038 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1159.67 seconds wall clock time: 23 minutes 33.71 seconds (1413.71 seconds total)