Starting phenix.real_space_refine (version: 1.20rc4) on Wed Dec 1 13:52:52 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgg_22326/12_2021/7jgg_22326.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgg_22326/12_2021/7jgg_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_22326/12_2021/7jgg_22326.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgg_22326/12_2021/7jgg_22326.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgg_22326/12_2021/7jgg_22326.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgg_22326/12_2021/7jgg_22326.pdb" } resolution = 4.88 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.20rc4-4434/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: 2.62, per 1000 atoms: 0.62 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 Amimo 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: 1.90 Conformation dependent library (CDL) restraints added in 568.0 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: 0.17 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: 1.06 Time building geometry restraints manager: 2.01 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 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. 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 Write .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: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.580 Check model and map are aligned: 0.050 Convert atoms to be neutral: 0.030 Process input model: 15.010 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.160 Set ADP refinement strategy: 0.000 Write .geo file: 0.000 Internal consistency checks: 0.000 Total: 24.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6419 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 : 54.13 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.27 % Favored : 96.53 % Rotamer Outliers : 0.00 % 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 *********************** 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 : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.1864 time to fit residues: 8.6836 Evaluate side-chains 26 residues out of total 463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.592 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8003 ------------------------------------------------------------------------------- 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: 4.9990 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2506 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6510 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 4264 Z= 0.199 Angle : 0.501 5.614 5710 Z= 0.281 Chirality : 0.035 0.237 581 Planarity : 0.004 0.030 728 Dihedral : 3.630 27.186 544 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 76.60 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.49 % Favored : 95.31 % Rotamer Outliers : 0.22 % 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: 2.03 (0.39), residues: 490 helix: 2.52 (0.29), residues: 316 sheet: None (None), residues: 0 loop : -0.97 (0.47), residues: 174 *********************** 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 32 residues out of total 463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 31 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 32 average time/residue: 0.1538 time to fit residues: 6.7128 Evaluate side-chains 26 residues out of total 463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.492 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6767 ------------------------------------------------------------------------------- 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: 0.0170 chunk 14 optimal weight: 0.4980 chunk 37 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 45 optimal weight: 0.0980 chunk 49 optimal weight: 3.9990 chunk 40 optimal weight: 0.0040 chunk 15 optimal weight: 4.9990 chunk 36 optimal weight: 20.0000 chunk 44 optimal weight: 5.9990 overall best weight: 0.2830 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6480 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.001 0.016 4264 Z= 0.091 Angle : 0.357 4.655 5710 Z= 0.202 Chirality : 0.032 0.126 581 Planarity : 0.002 0.024 728 Dihedral : 3.459 28.127 544 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 61.86 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.47 % Favored : 96.33 % Rotamer Outliers : 0.00 % 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: 2.64 (0.40), residues: 490 helix: 3.02 (0.29), residues: 310 sheet: None (None), residues: 0 loop : -0.63 (0.49), residues: 180 *********************** 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 32 residues out of total 463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.1725 time to fit residues: 7.5356 Evaluate side-chains 25 residues out of total 463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.586 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7881 ------------------------------------------------------------------------------- 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: 0.9990 chunk 23 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 43 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- 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 A2473 HIS ** A2506 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6577 moved from start: 0.3583 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= 0.230 Angle : 0.557 4.159 5710 Z= 0.320 Chirality : 0.035 0.126 581 Planarity : 0.004 0.034 728 Dihedral : 4.092 30.494 544 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 98.10 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.51 % Favored : 94.29 % Rotamer Outliers : 0.22 % 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: 1.21 (0.37), residues: 490 helix: 1.78 (0.27), residues: 323 sheet: None (None), residues: 0 loop : -1.18 (0.45), residues: 167 *********************** 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 31 residues out of total 463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 30 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 31 average time/residue: 0.1751 time to fit residues: 7.3979 Evaluate side-chains 25 residues out of total 463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.561 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7713 ------------------------------------------------------------------------------- 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: 5.9990 chunk 19 optimal weight: 20.0000 chunk 41 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 12 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 28 optimal weight: 5.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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: 0.6561 moved from start: 0.3697 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= 0.135 Angle : 0.419 3.949 5710 Z= 0.240 Chirality : 0.034 0.156 581 Planarity : 0.003 0.031 728 Dihedral : 3.937 29.980 544 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 81.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer Outliers : 0.00 % 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: 1.60 (0.38), residues: 490 helix: 2.18 (0.29), residues: 322 sheet: None (None), residues: 0 loop : -1.24 (0.46), residues: 168 *********************** 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 34 residues out of total 463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.1560 time to fit residues: 7.2762 Evaluate side-chains 27 residues out of total 463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.511 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7031 ------------------------------------------------------------------------------- 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: 3.9990 chunk 48 optimal weight: 6.9990 chunk 40 optimal weight: 30.0000 chunk 22 optimal weight: 10.0000 chunk 4 optimal weight: 0.0970 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 27 optimal weight: 8.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- 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: 0.6562 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.018 4264 Z= 0.141 Angle : 0.433 3.702 5710 Z= 0.247 Chirality : 0.033 0.124 581 Planarity : 0.003 0.033 728 Dihedral : 3.883 29.825 544 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 83.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer Outliers : 0.00 % 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: 1.53 (0.38), residues: 490 helix: 2.11 (0.29), residues: 323 sheet: None (None), residues: 0 loop : -1.25 (0.46), residues: 167 *********************** 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 : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1655 time to fit residues: 7.5210 Evaluate side-chains 24 residues out of total 463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.552 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7595 ------------------------------------------------------------------------------- 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: 7.9990 chunk 30 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 22 optimal weight: 9.9990 chunk 19 optimal weight: 30.0000 chunk 28 optimal weight: 8.9990 chunk 14 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 overall best weight: 2.2784 ------------------------------------------------------------------------------- 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: 0.6585 moved from start: 0.4776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 4264 Z= 0.171 Angle : 0.457 3.635 5710 Z= 0.262 Chirality : 0.034 0.118 581 Planarity : 0.003 0.035 728 Dihedral : 4.042 31.294 544 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 91.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer Outliers : 0.00 % 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: 1.37 (0.38), residues: 490 helix: 1.95 (0.29), residues: 323 sheet: None (None), residues: 0 loop : -1.24 (0.46), residues: 167 *********************** 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 33 residues out of total 463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1662 time to fit residues: 7.5142 Evaluate side-chains 24 residues out of total 463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.548 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7780 ------------------------------------------------------------------------------- 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: 0.0570 chunk 4 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 19 optimal weight: 30.0000 chunk 35 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 overall best weight: 2.0106 ------------------------------------------------------------------------------- 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: 0.6579 moved from start: 0.5163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 4264 Z= 0.154 Angle : 0.434 5.145 5710 Z= 0.249 Chirality : 0.033 0.124 581 Planarity : 0.003 0.039 728 Dihedral : 3.998 30.926 544 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 90.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer Outliers : 0.00 % 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: 1.32 (0.38), residues: 490 helix: 1.91 (0.29), residues: 322 sheet: None (None), residues: 0 loop : -1.24 (0.46), residues: 168 *********************** 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 33 residues out of total 463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1553 time to fit residues: 7.1629 Evaluate side-chains 25 residues out of total 463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.558 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7637 ------------------------------------------------------------------------------- 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: 10.0000 chunk 42 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 chunk 28 optimal weight: 0.0270 chunk 22 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 49 optimal weight: 0.3980 chunk 45 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.6840 ------------------------------------------------------------------------------- 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: 0.6546 moved from start: 0.5140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 4264 Z= 0.113 Angle : 0.409 4.695 5710 Z= 0.233 Chirality : 0.033 0.121 581 Planarity : 0.003 0.039 728 Dihedral : 3.882 29.769 544 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 80.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer Outliers : 0.00 % 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: 1.69 (0.39), residues: 490 helix: 2.15 (0.29), residues: 321 sheet: None (None), residues: 0 loop : -0.95 (0.48), residues: 169 *********************** 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 33 residues out of total 463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1682 time to fit residues: 7.6040 Evaluate side-chains 22 residues out of total 463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.552 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7926 ------------------------------------------------------------------------------- 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: 2.9990 chunk 30 optimal weight: 5.9990 chunk 24 optimal weight: 0.0040 chunk 31 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 36 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 39 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 overall best weight: 2.4000 ------------------------------------------------------------------------------- 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 ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6589 moved from start: 0.5884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 4264 Z= 0.179 Angle : 0.500 5.086 5710 Z= 0.284 Chirality : 0.035 0.120 581 Planarity : 0.004 0.043 728 Dihedral : 4.083 29.667 544 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 98.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer Outliers : 0.00 % 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: 1.21 (0.38), residues: 490 helix: 1.77 (0.29), residues: 323 sheet: None (None), residues: 0 loop : -1.15 (0.49), residues: 167 ********************** 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 30 residues out of total 463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.1615 time to fit residues: 6.7857 Evaluate side-chains 22 residues out of total 463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.555 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7637 ------------------------------------------------------------------------------- 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: 0.0030 chunk 5 optimal weight: 10.0000 chunk 7 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 chunk 2 optimal weight: 0.0980 chunk 28 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 30 optimal weight: 0.0980 overall best weight: 0.3790 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.058755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.049527 restraints weight = 62739.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.049798 restraints weight = 58781.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.049958 restraints weight = 55651.420| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3608 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3608 r_free = 0.3608 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3608 r_free = 0.3608 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3608 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.5677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.018 4264 Z= 0.106 Angle : 0.405 4.010 5710 Z= 0.229 Chirality : 0.033 0.122 581 Planarity : 0.003 0.040 728 Dihedral : 3.853 28.260 544 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 80.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer Outliers : 0.00 % 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: 1.72 (0.39), residues: 490 helix: 2.14 (0.29), residues: 316 sheet: None (None), residues: 0 loop : -0.78 (0.50), residues: 174 =============================================================================== Job complete usr+sys time: 1106.65 seconds wall clock time: 21 minutes 4.74 seconds (1264.74 seconds total)