Starting phenix.real_space_refine (version: dev) on Fri Feb 17 16:05:38 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7slq_25198/02_2023/7slq_25198_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7slq_25198/02_2023/7slq_25198.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7slq_25198/02_2023/7slq_25198.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7slq_25198/02_2023/7slq_25198.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7slq_25198/02_2023/7slq_25198_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7slq_25198/02_2023/7slq_25198_updated.pdb" } resolution = 3.7 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= 0.005 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 Process input model Symmetric amino acids flipped Residue "A ARG 433": "NH1" <-> "NH2" Residue "A ARG 443": "NH1" <-> "NH2" Residue "A ARG 469": "NH1" <-> "NH2" Residue "A ARG 488": "NH1" <-> "NH2" Residue "A ARG 531": "NH1" <-> "NH2" Residue "A ARG 601": "NH1" <-> "NH2" Residue "A ARG 608": "NH1" <-> "NH2" Residue "B ARG 55": "NH1" <-> "NH2" Residue "B ARG 548": "NH1" <-> "NH2" Residue "B ARG 552": "NH1" <-> "NH2" Residue "B GLU 562": "OE1" <-> "OE2" Residue "B ARG 565": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 5451 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1862 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 221} Chain breaks: 2 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 57 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 6, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 48 Chain: "B" Number of atoms: 2473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2473 Classifications: {'peptide': 321} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 10, 'TRANS': 310} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 9, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 72 Chain: "R" Number of atoms: 1090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 1090 Unusual residues: {'G5J': 1} Classifications: {'RNA': 50, 'undetermined': 1} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 16, 'rna3p_pyr': 21} Link IDs: {'rna2p': 12, 'rna3p': 37, None: 1} Not linked: pdbres="G5J R 1 " pdbres=" G R 2 " Chain breaks: 1 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Time building chain proxies: 4.05, per 1000 atoms: 0.74 Number of scatterers: 5451 At special positions: 0 Unit cell: (82.39, 92.02, 103.79, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 53 15.00 O 1157 8.00 N 958 7.00 C 3269 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.69 Conformation dependent library (CDL) restraints added in 677.5 milliseconds 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1054 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 4 sheets defined 41.3% alpha, 11.8% beta 13 base pairs and 21 stacking pairs defined. Time for finding SS restraints: 1.71 Creating SS restraints... Processing helix chain 'A' and resid 433 through 435 No H-bonds generated for 'chain 'A' and resid 433 through 435' Processing helix chain 'A' and resid 439 through 441 No H-bonds generated for 'chain 'A' and resid 439 through 441' Processing helix chain 'A' and resid 458 through 464 removed outlier: 4.008A pdb=" N LYS A 464 " --> pdb=" O SER A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 491 removed outlier: 3.852A pdb=" N HIS A 481 " --> pdb=" O SER A 477 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N SER A 482 " --> pdb=" O ARG A 478 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TYR A 490 " --> pdb=" O ASN A 486 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU A 491 " --> pdb=" O ILE A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 530 removed outlier: 3.793A pdb=" N SER A 530 " --> pdb=" O SER A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 569 Processing helix chain 'A' and resid 584 through 606 removed outlier: 7.969A pdb=" N ASP A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) removed outlier: 8.839A pdb=" N GLU A 594 " --> pdb=" O ASN A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 626 Processing helix chain 'A' and resid 631 through 637 Processing helix chain 'A' and resid 647 through 650 No H-bonds generated for 'chain 'A' and resid 647 through 650' Processing helix chain 'B' and resid 30 through 45 Processing helix chain 'B' and resid 48 through 53 Processing helix chain 'B' and resid 56 through 62 Processing helix chain 'B' and resid 71 through 75 Processing helix chain 'B' and resid 78 through 81 No H-bonds generated for 'chain 'B' and resid 78 through 81' Processing helix chain 'B' and resid 87 through 93 Processing helix chain 'B' and resid 121 through 125 Processing helix chain 'B' and resid 138 through 146 Processing helix chain 'B' and resid 177 through 185 removed outlier: 3.586A pdb=" N GLU B 184 " --> pdb=" O ALA B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 412 Processing helix chain 'B' and resid 468 through 476 Processing helix chain 'B' and resid 500 through 507 Processing helix chain 'B' and resid 527 through 545 Processing helix chain 'B' and resid 553 through 570 Processing sheet with id= A, first strand: chain 'A' and resid 660 through 663 removed outlier: 3.511A pdb=" N SER A 660 " --> pdb=" O HIS A 682 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU A 616 " --> pdb=" O CYS A 580 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N LEU A 581 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ARG A 469 " --> pdb=" O VAL A 447 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N ASP A 449 " --> pdb=" O ARG A 469 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL A 471 " --> pdb=" O ASP A 449 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL A 554 " --> pdb=" O GLY A 472 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N ASP A 474 " --> pdb=" O VAL A 554 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL A 556 " --> pdb=" O ASP A 474 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 68 through 70 removed outlier: 3.673A pdb=" N VAL B 69 " --> pdb=" O ILE B 109 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 377 through 380 removed outlier: 3.558A pdb=" N ARG B 377 " --> pdb=" O GLU B 130 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR B 153 " --> pdb=" O GLU B 172 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 519 through 523 166 hydrogen bonds defined for protein. 489 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 34 hydrogen bonds 68 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 21 stacking parallelities Total time for adding SS restraints: 1.88 Time building geometry restraints manager: 2.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1016 1.33 - 1.45: 1622 1.45 - 1.57: 2902 1.57 - 1.69: 106 1.69 - 1.81: 22 Bond restraints: 5668 Sorted by residual: bond pdb=" C3' G5J R 1 " pdb=" O3' G5J R 1 " ideal model delta sigma weight residual 1.404 1.737 -0.333 2.00e-02 2.50e+03 2.78e+02 bond pdb=" C3' G5J R 1 " pdb=" C4' G5J R 1 " ideal model delta sigma weight residual 1.526 1.248 0.278 2.00e-02 2.50e+03 1.93e+02 bond pdb=" C1' G5J R 1 " pdb=" C2' G5J R 1 " ideal model delta sigma weight residual 1.524 1.254 0.270 2.00e-02 2.50e+03 1.82e+02 bond pdb=" C6 G5J R 1 " pdb=" O6 G5J R 1 " ideal model delta sigma weight residual 1.226 1.433 -0.207 2.00e-02 2.50e+03 1.07e+02 bond pdb=" C2' G5J R 1 " pdb=" C3' G5J R 1 " ideal model delta sigma weight residual 1.531 1.722 -0.191 2.00e-02 2.50e+03 9.15e+01 ... (remaining 5663 not shown) Histogram of bond angle deviations from ideal: 91.52 - 101.07: 19 101.07 - 110.62: 2058 110.62 - 120.17: 3512 120.17 - 129.72: 2277 129.72 - 139.28: 58 Bond angle restraints: 7924 Sorted by residual: angle pdb=" C VAL B 99 " pdb=" N VAL B 100 " pdb=" CA VAL B 100 " ideal model delta sigma weight residual 121.97 128.13 -6.16 1.00e+00 1.00e+00 3.80e+01 angle pdb=" O3' A R 298 " pdb=" C3' A R 298 " pdb=" C2' A R 298 " ideal model delta sigma weight residual 109.50 118.39 -8.89 1.50e+00 4.44e-01 3.51e+01 angle pdb=" N TYR B 68 " pdb=" CA TYR B 68 " pdb=" CB TYR B 68 " ideal model delta sigma weight residual 111.05 102.42 8.63 1.50e+00 4.44e-01 3.31e+01 angle pdb=" O3A G5J R 1 " pdb=" PB G5J R 1 " pdb=" O3B G5J R 1 " ideal model delta sigma weight residual 92.82 109.77 -16.95 3.00e+00 1.11e-01 3.19e+01 angle pdb=" C4' G R 300 " pdb=" C3' G R 300 " pdb=" O3' G R 300 " ideal model delta sigma weight residual 109.40 117.58 -8.18 1.50e+00 4.44e-01 2.98e+01 ... (remaining 7919 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.50: 3168 34.50 - 69.00: 79 69.00 - 103.50: 7 103.50 - 138.00: 1 138.00 - 172.50: 2 Dihedral angle restraints: 3257 sinusoidal: 1628 harmonic: 1629 Sorted by residual: dihedral pdb=" C5' A R 298 " pdb=" C4' A R 298 " pdb=" C3' A R 298 " pdb=" O3' A R 298 " ideal model delta sinusoidal sigma weight residual 147.00 105.99 41.01 1 8.00e+00 1.56e-02 3.68e+01 dihedral pdb=" CA ASN B 135 " pdb=" C ASN B 135 " pdb=" N VAL B 136 " pdb=" CA VAL B 136 " ideal model delta harmonic sigma weight residual -180.00 -155.10 -24.90 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" O4' A R 296 " pdb=" C1' A R 296 " pdb=" N9 A R 296 " pdb=" C4 A R 296 " ideal model delta sinusoidal sigma weight residual -106.00 -171.42 65.42 1 1.70e+01 3.46e-03 1.94e+01 ... (remaining 3254 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 875 0.118 - 0.237: 54 0.237 - 0.355: 2 0.355 - 0.473: 2 0.473 - 0.591: 1 Chirality restraints: 934 Sorted by residual: chirality pdb=" C3' A R 298 " pdb=" C4' A R 298 " pdb=" O3' A R 298 " pdb=" C2' A R 298 " both_signs ideal model delta sigma weight residual False -2.74 -2.15 -0.59 2.00e-01 2.50e+01 8.75e+00 chirality pdb=" CA PRO A 427 " pdb=" N PRO A 427 " pdb=" C PRO A 427 " pdb=" CB PRO A 427 " both_signs ideal model delta sigma weight residual False 2.72 2.31 0.41 2.00e-01 2.50e+01 4.23e+00 chirality pdb=" C3' G5J R 1 " pdb=" C2' G5J R 1 " pdb=" C4' G5J R 1 " pdb=" O3' G5J R 1 " both_signs ideal model delta sigma weight residual False -2.71 -3.10 0.39 2.00e-01 2.50e+01 3.80e+00 ... (remaining 931 not shown) Planarity restraints: 815 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 549 " -0.045 5.00e-02 4.00e+02 6.91e-02 7.63e+00 pdb=" N PRO A 550 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO A 550 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 550 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G5J R 1 " -0.031 2.00e-02 2.50e+03 1.47e-02 6.50e+00 pdb=" C2 G5J R 1 " -0.001 2.00e-02 2.50e+03 pdb=" C4 G5J R 1 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G5J R 1 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G5J R 1 " -0.000 2.00e-02 2.50e+03 pdb=" C8 G5J R 1 " 0.011 2.00e-02 2.50e+03 pdb=" N1 G5J R 1 " 0.000 2.00e-02 2.50e+03 pdb=" N2 G5J R 1 " 0.010 2.00e-02 2.50e+03 pdb=" N3 G5J R 1 " -0.000 2.00e-02 2.50e+03 pdb=" N7 G5J R 1 " 0.026 2.00e-02 2.50e+03 pdb=" N9 G5J R 1 " 0.011 2.00e-02 2.50e+03 pdb=" O6 G5J R 1 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 132 " -0.037 5.00e-02 4.00e+02 5.69e-02 5.17e+00 pdb=" N PRO B 133 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO B 133 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 133 " -0.032 5.00e-02 4.00e+02 ... (remaining 812 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 185 2.69 - 3.25: 4874 3.25 - 3.80: 8785 3.80 - 4.35: 10870 4.35 - 4.90: 17241 Nonbonded interactions: 41955 Sorted by model distance: nonbonded pdb=" O2' A R 297 " pdb=" OP1 A R 298 " model vdw 2.144 2.440 nonbonded pdb=" O GLY A 532 " pdb=" OH TYR B 391 " model vdw 2.239 2.440 nonbonded pdb=" O SER B 461 " pdb=" OG1 THR B 491 " model vdw 2.331 2.440 nonbonded pdb=" O TYR A 650 " pdb=" OG SER A 653 " model vdw 2.337 2.440 nonbonded pdb=" OD1 ASP A 474 " pdb=" O2' SAH A 701 " model vdw 2.341 2.440 ... (remaining 41950 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 P 53 5.49 5 S 14 5.16 5 C 3269 2.51 5 N 958 2.21 5 O 1157 1.98 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=1.00 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: 0.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 2.460 Check model and map are aligned: 0.080 Process input model: 20.390 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.050 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 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 : 0.011 0.333 5668 Z= 0.790 Angle : 1.161 16.945 7924 Z= 0.628 Chirality : 0.062 0.591 934 Planarity : 0.007 0.069 815 Dihedral : 14.972 172.502 2203 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer Outliers : 1.35 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 4.00 % 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: -2.83 (0.30), residues: 546 helix: -2.16 (0.25), residues: 252 sheet: -0.52 (0.63), residues: 64 loop : -1.76 (0.35), residues: 230 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 105 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 109 average time/residue: 0.2436 time to fit residues: 32.4066 Evaluate side-chains 55 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 53 time to evaluate : 0.589 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1891 time to fit residues: 1.1853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 0.0570 chunk 45 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 chunk 30 optimal weight: 7.9990 chunk 24 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 28 optimal weight: 8.9990 chunk 35 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 514 ASN B 528 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 5668 Z= 0.162 Angle : 0.563 7.488 7924 Z= 0.292 Chirality : 0.038 0.189 934 Planarity : 0.005 0.080 815 Dihedral : 15.034 173.744 1209 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer Outliers : 2.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.47 (0.32), residues: 546 helix: -0.68 (0.30), residues: 257 sheet: -0.04 (0.75), residues: 47 loop : -1.40 (0.35), residues: 242 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 63 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 69 average time/residue: 0.2015 time to fit residues: 18.0941 Evaluate side-chains 54 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 47 time to evaluate : 0.531 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1073 time to fit residues: 1.7549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 8.9990 chunk 16 optimal weight: 4.9990 chunk 45 optimal weight: 0.5980 chunk 37 optimal weight: 0.4980 chunk 15 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 18 optimal weight: 0.0370 chunk 43 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 overall best weight: 0.8060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 514 ASN B 530 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 5668 Z= 0.153 Angle : 0.527 6.503 7924 Z= 0.274 Chirality : 0.037 0.178 934 Planarity : 0.005 0.081 815 Dihedral : 14.714 174.185 1209 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer Outliers : 1.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.57 (0.34), residues: 546 helix: 0.29 (0.32), residues: 249 sheet: 0.78 (0.75), residues: 52 loop : -1.32 (0.36), residues: 245 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 53 time to evaluate : 0.581 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 58 average time/residue: 0.1859 time to fit residues: 14.5528 Evaluate side-chains 44 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 42 time to evaluate : 0.620 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0594 time to fit residues: 1.0130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 0.9980 chunk 28 optimal weight: 9.9990 chunk 6 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 57 optimal weight: 7.9990 chunk 51 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 5668 Z= 0.183 Angle : 0.529 8.500 7924 Z= 0.272 Chirality : 0.037 0.166 934 Planarity : 0.005 0.081 815 Dihedral : 14.510 174.466 1209 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer Outliers : 3.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.30 (0.35), residues: 546 helix: 0.59 (0.33), residues: 248 sheet: 0.43 (0.80), residues: 47 loop : -1.09 (0.37), residues: 251 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 49 time to evaluate : 0.514 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 58 average time/residue: 0.1812 time to fit residues: 13.9053 Evaluate side-chains 48 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 41 time to evaluate : 0.597 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0676 time to fit residues: 1.4986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 7.9990 chunk 43 optimal weight: 50.0000 chunk 23 optimal weight: 0.7980 chunk 49 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 682 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 5668 Z= 0.256 Angle : 0.581 7.237 7924 Z= 0.298 Chirality : 0.039 0.165 934 Planarity : 0.005 0.081 815 Dihedral : 14.556 174.701 1209 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer Outliers : 2.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.30 (0.35), residues: 546 helix: 0.62 (0.33), residues: 250 sheet: 0.78 (0.74), residues: 54 loop : -1.30 (0.37), residues: 242 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 47 time to evaluate : 0.613 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 53 average time/residue: 0.1634 time to fit residues: 12.0759 Evaluate side-chains 44 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 41 time to evaluate : 0.607 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1582 time to fit residues: 1.3149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 0.6980 chunk 58 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 0.3980 chunk 4 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 0.2980 chunk 55 optimal weight: 9.9990 chunk 6 optimal weight: 0.7980 chunk 33 optimal weight: 0.4980 chunk 42 optimal weight: 9.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 5668 Z= 0.136 Angle : 0.517 10.852 7924 Z= 0.258 Chirality : 0.036 0.149 934 Planarity : 0.005 0.083 815 Dihedral : 14.370 175.664 1209 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer Outliers : 2.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.06 (0.36), residues: 546 helix: 0.85 (0.34), residues: 249 sheet: 0.44 (0.77), residues: 51 loop : -1.06 (0.38), residues: 246 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 45 time to evaluate : 0.620 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 52 average time/residue: 0.1441 time to fit residues: 10.7256 Evaluate side-chains 47 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 42 time to evaluate : 0.580 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0650 time to fit residues: 1.2871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 36 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 39 optimal weight: 0.0670 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 5668 Z= 0.147 Angle : 0.510 9.201 7924 Z= 0.258 Chirality : 0.036 0.154 934 Planarity : 0.005 0.089 815 Dihedral : 14.199 174.854 1209 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer Outliers : 2.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.02 (0.36), residues: 546 helix: 0.96 (0.34), residues: 248 sheet: 0.47 (0.77), residues: 51 loop : -1.05 (0.38), residues: 247 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 47 time to evaluate : 0.547 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 54 average time/residue: 0.1380 time to fit residues: 10.8489 Evaluate side-chains 47 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 41 time to evaluate : 0.709 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0749 time to fit residues: 1.4190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 45 optimal weight: 0.0970 chunk 52 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 50 optimal weight: 6.9990 chunk 53 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 42 optimal weight: 0.0030 chunk 16 optimal weight: 3.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 618 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.3977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 5668 Z= 0.152 Angle : 0.505 9.098 7924 Z= 0.258 Chirality : 0.036 0.153 934 Planarity : 0.005 0.089 815 Dihedral : 14.130 174.456 1209 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer Outliers : 0.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.22 (0.36), residues: 546 helix: 1.07 (0.34), residues: 248 sheet: 0.89 (0.72), residues: 61 loop : -1.04 (0.39), residues: 237 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 43 time to evaluate : 0.696 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 46 average time/residue: 0.1697 time to fit residues: 11.0667 Evaluate side-chains 43 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 41 time to evaluate : 0.589 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0835 time to fit residues: 1.0258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 35 optimal weight: 0.0980 chunk 56 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 27 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 55 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.4179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 5668 Z= 0.309 Angle : 0.628 6.803 7924 Z= 0.324 Chirality : 0.040 0.158 934 Planarity : 0.006 0.095 815 Dihedral : 14.406 173.831 1209 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer Outliers : 1.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.28 (0.35), residues: 546 helix: 0.59 (0.32), residues: 249 sheet: 0.57 (0.77), residues: 54 loop : -1.16 (0.37), residues: 243 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 46 time to evaluate : 0.555 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 49 average time/residue: 0.1360 time to fit residues: 9.7515 Evaluate side-chains 41 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 38 time to evaluate : 0.554 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0622 time to fit residues: 1.0793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 0.9980 chunk 36 optimal weight: 0.2980 chunk 29 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 50 optimal weight: 20.0000 chunk 14 optimal weight: 3.9990 chunk 43 optimal weight: 20.0000 chunk 7 optimal weight: 1.9990 chunk 13 optimal weight: 0.0770 chunk 47 optimal weight: 4.9990 chunk 19 optimal weight: 9.9990 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.4274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 5668 Z= 0.164 Angle : 0.542 10.938 7924 Z= 0.273 Chirality : 0.036 0.146 934 Planarity : 0.005 0.094 815 Dihedral : 14.219 175.065 1209 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.05 (0.36), residues: 546 helix: 0.84 (0.33), residues: 249 sheet: 0.29 (0.78), residues: 51 loop : -0.98 (0.38), residues: 246 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 42 time to evaluate : 0.598 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 43 average time/residue: 0.1719 time to fit residues: 10.3015 Evaluate side-chains 39 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 38 time to evaluate : 0.543 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0822 time to fit residues: 0.8179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 8.9990 chunk 6 optimal weight: 0.7980 chunk 8 optimal weight: 0.4980 chunk 41 optimal weight: 0.7980 chunk 2 optimal weight: 0.0370 chunk 34 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 1 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 417 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 = 0.4437 r_free = 0.4437 target = 0.174192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.136543 restraints weight = 9617.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.135781 restraints weight = 9387.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.138291 restraints weight = 8122.988| |-----------------------------------------------------------------------------| r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.4388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 5668 Z= 0.143 Angle : 0.509 6.946 7924 Z= 0.259 Chirality : 0.036 0.142 934 Planarity : 0.005 0.094 815 Dihedral : 14.088 174.144 1209 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.18 (0.36), residues: 546 helix: 1.10 (0.34), residues: 241 sheet: 0.43 (0.78), residues: 51 loop : -0.90 (0.38), residues: 254 =============================================================================== Job complete usr+sys time: 1169.02 seconds wall clock time: 22 minutes 4.37 seconds (1324.37 seconds total)