Sun 23 Dec 22:23:05 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2ozj-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ozj-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ozj-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ozj-3.6-parrot-hancs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ozj-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ozj-3.6-parrot-hancs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Sun 23 Dec 22:23:15 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ozj-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ozj-3.6-parrot-hancs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 138 and 0 Target number of residues in the AU: 138 Target solvent content: 0.6528 Checking the provided sequence file Detected sequence length: 114 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 228 Adjusted target solvent content: 0.43 Input MTZ file: 2ozj-3.6-parrot-hancs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 20 Cell parameters: 40.940 69.810 150.550 90.000 90.000 90.000 Input sequence file: 2ozj-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 1824 target number of atoms Had to go as low as 0.60 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 75.275 3.600 Wilson plot Bfac: 79.88 2686 reflections ( 99.26 % complete ) and 0 restraints for refining 2033 atoms. Observations/parameters ratio is 0.33 ------------------------------------------------------ Starting model: R = 0.3263 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2961 (Rfree = 0.000) for 2033 atoms. Found 9 (13 requested) and removed 13 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.49 3.83 Search for helices and strands: 0 residues in 0 chains, 2046 seeds are put forward NCS extension: 0 residues added, 2046 seeds are put forward Round 1: 84 peptides, 16 chains. Longest chain 9 peptides. Score 0.338 Round 2: 123 peptides, 16 chains. Longest chain 30 peptides. Score 0.600 Round 3: 129 peptides, 16 chains. Longest chain 25 peptides. Score 0.632 Round 4: 143 peptides, 18 chains. Longest chain 19 peptides. Score 0.657 Round 5: 138 peptides, 18 chains. Longest chain 20 peptides. Score 0.632 Taking the results from Round 4 Chains 18, Residues 125, Estimated correctness of the model 35.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2686 reflections ( 99.26 % complete ) and 3603 restraints for refining 1653 atoms. 3121 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2788 (Rfree = 0.000) for 1653 atoms. Found 7 (10 requested) and removed 14 (5 requested) atoms. Cycle 2: After refmac, R = 0.2714 (Rfree = 0.000) for 1600 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Cycle 3: After refmac, R = 0.2656 (Rfree = 0.000) for 1567 atoms. Found 8 (10 requested) and removed 8 (5 requested) atoms. Cycle 4: After refmac, R = 0.2674 (Rfree = 0.000) for 1553 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 5: After refmac, R = 0.2430 (Rfree = 0.000) for 1544 atoms. Found 4 (9 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.50 3.84 Search for helices and strands: 0 residues in 0 chains, 1612 seeds are put forward NCS extension: 21 residues added (3 deleted due to clashes), 1633 seeds are put forward Round 1: 114 peptides, 22 chains. Longest chain 8 peptides. Score 0.374 Round 2: 129 peptides, 20 chains. Longest chain 14 peptides. Score 0.533 Round 3: 122 peptides, 17 chains. Longest chain 19 peptides. Score 0.569 Round 4: 135 peptides, 18 chains. Longest chain 21 peptides. Score 0.616 Round 5: 137 peptides, 17 chains. Longest chain 18 peptides. Score 0.649 Taking the results from Round 5 Chains 17, Residues 120, Estimated correctness of the model 32.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2686 reflections ( 99.26 % complete ) and 3333 restraints for refining 1554 atoms. 2870 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2840 (Rfree = 0.000) for 1554 atoms. Found 7 (9 requested) and removed 20 (4 requested) atoms. Cycle 7: After refmac, R = 0.2466 (Rfree = 0.000) for 1522 atoms. Found 8 (9 requested) and removed 47 (4 requested) atoms. Cycle 8: After refmac, R = 0.2985 (Rfree = 0.000) for 1472 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. Cycle 9: After refmac, R = 0.3629 (Rfree = 0.000) for 1460 atoms. Found 9 (9 requested) and removed 50 (4 requested) atoms. Cycle 10: After refmac, R = 0.3147 (Rfree = 0.000) for 1396 atoms. Found 5 (9 requested) and removed 32 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 4.43 4.87 Search for helices and strands: 0 residues in 0 chains, 1452 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 1472 seeds are put forward Round 1: 78 peptides, 18 chains. Longest chain 6 peptides. Score 0.219 Round 2: 92 peptides, 15 chains. Longest chain 13 peptides. Score 0.431 Round 3: 93 peptides, 16 chains. Longest chain 15 peptides. Score 0.407 Round 4: 103 peptides, 17 chains. Longest chain 11 peptides. Score 0.448 Round 5: 95 peptides, 16 chains. Longest chain 16 peptides. Score 0.421 Taking the results from Round 4 Chains 17, Residues 86, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2686 reflections ( 99.26 % complete ) and 3272 restraints for refining 1463 atoms. 2945 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3234 (Rfree = 0.000) for 1463 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 12: After refmac, R = 0.3200 (Rfree = 0.000) for 1442 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. Cycle 13: After refmac, R = 0.3179 (Rfree = 0.000) for 1440 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 14: After refmac, R = 0.3339 (Rfree = 0.000) for 1435 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 15: After refmac, R = 0.2903 (Rfree = 0.000) for 1422 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.49 3.83 Search for helices and strands: 0 residues in 0 chains, 1474 seeds are put forward NCS extension: 0 residues added, 1474 seeds are put forward Round 1: 77 peptides, 17 chains. Longest chain 7 peptides. Score 0.246 Round 2: 109 peptides, 19 chains. Longest chain 9 peptides. Score 0.429 Round 3: 98 peptides, 17 chains. Longest chain 12 peptides. Score 0.412 Round 4: 105 peptides, 18 chains. Longest chain 13 peptides. Score 0.431 Round 5: 104 peptides, 16 chains. Longest chain 14 peptides. Score 0.484 Taking the results from Round 5 Chains 16, Residues 88, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 2686 reflections ( 99.26 % complete ) and 3394 restraints for refining 1523 atoms. 3041 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3147 (Rfree = 0.000) for 1523 atoms. Found 8 (9 requested) and removed 22 (4 requested) atoms. Cycle 17: After refmac, R = 0.3568 (Rfree = 0.000) for 1490 atoms. Found 9 (9 requested) and removed 32 (4 requested) atoms. Cycle 18: After refmac, R = 0.3430 (Rfree = 0.000) for 1452 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 19: After refmac, R = 0.2972 (Rfree = 0.000) for 1444 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 20: After refmac, R = 0.2844 (Rfree = 0.000) for 1434 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.48 3.82 Search for helices and strands: 0 residues in 0 chains, 1496 seeds are put forward NCS extension: 0 residues added, 1496 seeds are put forward Round 1: 69 peptides, 13 chains. Longest chain 9 peptides. Score 0.320 Round 2: 85 peptides, 15 chains. Longest chain 10 peptides. Score 0.379 Round 3: 86 peptides, 14 chains. Longest chain 10 peptides. Score 0.419 Round 4: 83 peptides, 14 chains. Longest chain 10 peptides. Score 0.397 Round 5: 79 peptides, 14 chains. Longest chain 10 peptides. Score 0.366 Taking the results from Round 3 Chains 14, Residues 72, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2686 reflections ( 99.26 % complete ) and 3170 restraints for refining 1430 atoms. 2896 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3473 (Rfree = 0.000) for 1430 atoms. Found 9 (9 requested) and removed 26 (4 requested) atoms. Cycle 22: After refmac, R = 0.3064 (Rfree = 0.000) for 1393 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 23: After refmac, R = 0.2933 (Rfree = 0.000) for 1385 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 24: After refmac, R = 0.3312 (Rfree = 0.000) for 1375 atoms. Found 8 (8 requested) and removed 14 (4 requested) atoms. Cycle 25: After refmac, R = 0.3229 (Rfree = 0.000) for 1363 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.54 3.89 Search for helices and strands: 0 residues in 0 chains, 1408 seeds are put forward NCS extension: 0 residues added, 1408 seeds are put forward Round 1: 70 peptides, 15 chains. Longest chain 8 peptides. Score 0.257 Round 2: 84 peptides, 14 chains. Longest chain 11 peptides. Score 0.404 Round 3: 90 peptides, 15 chains. Longest chain 15 peptides. Score 0.416 Round 4: 91 peptides, 16 chains. Longest chain 9 peptides. Score 0.392 Round 5: 91 peptides, 13 chains. Longest chain 17 peptides. Score 0.486 Taking the results from Round 5 Chains 13, Residues 78, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2686 reflections ( 99.26 % complete ) and 3032 restraints for refining 1409 atoms. 2733 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3565 (Rfree = 0.000) for 1409 atoms. Found 9 (9 requested) and removed 22 (4 requested) atoms. Cycle 27: After refmac, R = 0.2956 (Rfree = 0.000) for 1380 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 28: After refmac, R = 0.3227 (Rfree = 0.000) for 1374 atoms. Found 8 (8 requested) and removed 19 (4 requested) atoms. Cycle 29: After refmac, R = 0.2848 (Rfree = 0.000) for 1353 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 30: After refmac, R = 0.3528 (Rfree = 0.000) for 1349 atoms. Found 8 (8 requested) and removed 18 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.77 4.14 Search for helices and strands: 0 residues in 0 chains, 1382 seeds are put forward NCS extension: 0 residues added, 1382 seeds are put forward Round 1: 52 peptides, 11 chains. Longest chain 7 peptides. Score 0.245 Round 2: 68 peptides, 14 chains. Longest chain 9 peptides. Score 0.276 Round 3: 65 peptides, 11 chains. Longest chain 9 peptides. Score 0.358 Round 4: 71 peptides, 12 chains. Longest chain 10 peptides. Score 0.371 Round 5: 69 peptides, 11 chains. Longest chain 11 peptides. Score 0.390 Taking the results from Round 5 Chains 11, Residues 58, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2686 reflections ( 99.26 % complete ) and 3031 restraints for refining 1374 atoms. 2810 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3433 (Rfree = 0.000) for 1374 atoms. Found 8 (8 requested) and removed 18 (4 requested) atoms. Cycle 32: After refmac, R = 0.3651 (Rfree = 0.000) for 1357 atoms. Found 8 (8 requested) and removed 17 (4 requested) atoms. Cycle 33: After refmac, R = 0.3305 (Rfree = 0.000) for 1343 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 34: After refmac, R = 0.3273 (Rfree = 0.000) for 1334 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 35: After refmac, R = 0.3178 (Rfree = 0.000) for 1333 atoms. Found 6 (8 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.59 3.94 Search for helices and strands: 0 residues in 0 chains, 1363 seeds are put forward NCS extension: 0 residues added, 1363 seeds are put forward Round 1: 40 peptides, 9 chains. Longest chain 6 peptides. Score 0.210 Round 2: 60 peptides, 12 chains. Longest chain 8 peptides. Score 0.280 Round 3: 56 peptides, 11 chains. Longest chain 7 peptides. Score 0.282 Round 4: 66 peptides, 12 chains. Longest chain 8 peptides. Score 0.331 Round 5: 68 peptides, 12 chains. Longest chain 11 peptides. Score 0.347 Taking the results from Round 5 Chains 12, Residues 56, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2686 reflections ( 99.26 % complete ) and 2731 restraints for refining 1295 atoms. 2519 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3189 (Rfree = 0.000) for 1295 atoms. Found 6 (8 requested) and removed 12 (4 requested) atoms. Cycle 37: After refmac, R = 0.2989 (Rfree = 0.000) for 1281 atoms. Found 7 (8 requested) and removed 7 (4 requested) atoms. Cycle 38: After refmac, R = 0.3296 (Rfree = 0.000) for 1278 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 39: After refmac, R = 0.3022 (Rfree = 0.000) for 1264 atoms. Found 5 (8 requested) and removed 9 (4 requested) atoms. Cycle 40: After refmac, R = 0.2983 (Rfree = 0.000) for 1252 atoms. Found 8 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.48 3.82 Search for helices and strands: 0 residues in 0 chains, 1290 seeds are put forward NCS extension: 0 residues added, 1290 seeds are put forward Round 1: 61 peptides, 14 chains. Longest chain 7 peptides. Score 0.214 Round 2: 57 peptides, 12 chains. Longest chain 7 peptides. Score 0.253 Round 3: 56 peptides, 11 chains. Longest chain 10 peptides. Score 0.282 Round 4: 60 peptides, 11 chains. Longest chain 8 peptides. Score 0.317 Round 5: 54 peptides, 9 chains. Longest chain 11 peptides. Score 0.341 Taking the results from Round 5 Chains 9, Residues 45, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2686 reflections ( 99.26 % complete ) and 2765 restraints for refining 1246 atoms. 2594 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3451 (Rfree = 0.000) for 1246 atoms. Found 7 (7 requested) and removed 19 (3 requested) atoms. Cycle 42: After refmac, R = 0.3026 (Rfree = 0.000) for 1230 atoms. Found 5 (7 requested) and removed 11 (3 requested) atoms. Cycle 43: After refmac, R = 0.3541 (Rfree = 0.000) for 1221 atoms. Found 7 (7 requested) and removed 13 (3 requested) atoms. Cycle 44: After refmac, R = 0.2971 (Rfree = 0.000) for 1207 atoms. Found 4 (7 requested) and removed 7 (3 requested) atoms. Cycle 45: After refmac, R = 0.3712 (Rfree = 0.000) for 1202 atoms. Found 7 (7 requested) and removed 19 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.57 3.92 Search for helices and strands: 0 residues in 0 chains, 1232 seeds are put forward NCS extension: 0 residues added, 1232 seeds are put forward Round 1: 34 peptides, 8 chains. Longest chain 5 peptides. Score 0.190 Round 2: 43 peptides, 8 chains. Longest chain 8 peptides. Score 0.282 Round 3: 44 peptides, 8 chains. Longest chain 8 peptides. Score 0.292 Round 4: 45 peptides, 8 chains. Longest chain 8 peptides. Score 0.301 Round 5: 45 peptides, 8 chains. Longest chain 8 peptides. Score 0.301 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 8, Residues 37, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2ozj-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2686 reflections ( 99.26 % complete ) and 2396 restraints for refining 1150 atoms. 2256 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2962 (Rfree = 0.000) for 1150 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.3379 (Rfree = 0.000) for 1141 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.3182 (Rfree = 0.000) for 1134 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.3326 (Rfree = 0.000) for 1124 atoms. TimeTaking 29.03