Sun 23 Dec 22:22:43 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 2pg3-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pg3-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pg3-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pg3-3.8-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/2pg3-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pg3-3.8-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 22:22:53 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/2pg3-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pg3-3.8-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 145 and 0 Target number of residues in the AU: 145 Target solvent content: 0.6695 Checking the provided sequence file Detected sequence length: 232 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 232 Adjusted target solvent content: 0.47 Input MTZ file: 2pg3-3.8-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: 92 Cell parameters: 78.154 78.154 77.755 90.000 90.000 90.000 Input sequence file: 2pg3-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 1856 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 Loops will be built when appropriate and at the last cycle Resolution range: 27.561 3.801 Wilson plot Bfac: 91.23 2610 reflections ( 99.58 % complete ) and 0 restraints for refining 2045 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.3888 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3720 (Rfree = 0.000) for 2045 atoms. Found 11 (11 requested) and removed 20 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.73 3.88 Search for helices and strands: 0 residues in 0 chains, 2070 seeds are put forward Round 1: 43 peptides, 10 chains. Longest chain 5 peptides. Score 0.196 Round 2: 50 peptides, 11 chains. Longest chain 6 peptides. Score 0.223 Round 3: 53 peptides, 11 chains. Longest chain 7 peptides. Score 0.249 Round 4: 62 peptides, 13 chains. Longest chain 6 peptides. Score 0.254 Round 5: 69 peptides, 14 chains. Longest chain 7 peptides. Score 0.276 Taking the results from Round 5 Chains 14, Residues 55, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2610 reflections ( 99.58 % complete ) and 4303 restraints for refining 1679 atoms. 4097 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3589 (Rfree = 0.000) for 1679 atoms. Found 9 (9 requested) and removed 16 (4 requested) atoms. Cycle 2: After refmac, R = 0.3343 (Rfree = 0.000) for 1647 atoms. Found 8 (9 requested) and removed 20 (4 requested) atoms. Cycle 3: After refmac, R = 0.3248 (Rfree = 0.000) for 1612 atoms. Found 1 (8 requested) and removed 11 (4 requested) atoms. Cycle 4: After refmac, R = 0.2606 (Rfree = 0.000) for 1591 atoms. Found 4 (8 requested) and removed 9 (4 requested) atoms. Cycle 5: After refmac, R = 0.2817 (Rfree = 0.000) for 1581 atoms. Found 2 (8 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.70 3.85 Search for helices and strands: 0 residues in 0 chains, 1624 seeds are put forward Round 1: 62 peptides, 14 chains. Longest chain 6 peptides. Score 0.219 Round 2: 70 peptides, 13 chains. Longest chain 9 peptides. Score 0.317 Round 3: 69 peptides, 14 chains. Longest chain 7 peptides. Score 0.276 Round 4: 77 peptides, 15 chains. Longest chain 8 peptides. Score 0.305 Round 5: 70 peptides, 12 chains. Longest chain 8 peptides. Score 0.350 Taking the results from Round 5 Chains 12, Residues 58, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2610 reflections ( 99.58 % complete ) and 3633 restraints for refining 1517 atoms. 3413 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2811 (Rfree = 0.000) for 1517 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 7: After refmac, R = 0.2752 (Rfree = 0.000) for 1505 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. Cycle 8: After refmac, R = 0.2911 (Rfree = 0.000) for 1492 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 9: After refmac, R = 0.2610 (Rfree = 0.000) for 1484 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 10: After refmac, R = 0.2820 (Rfree = 0.000) for 1475 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.71 3.86 Search for helices and strands: 0 residues in 0 chains, 1539 seeds are put forward Round 1: 74 peptides, 16 chains. Longest chain 7 peptides. Score 0.249 Round 2: 79 peptides, 13 chains. Longest chain 12 peptides. Score 0.383 Round 3: 79 peptides, 15 chains. Longest chain 8 peptides. Score 0.320 Round 4: 77 peptides, 15 chains. Longest chain 7 peptides. Score 0.305 Round 5: 83 peptides, 15 chains. Longest chain 8 peptides. Score 0.350 Taking the results from Round 2 Chains 13, Residues 66, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 2610 reflections ( 99.58 % complete ) and 3207 restraints for refining 1448 atoms. 2938 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2847 (Rfree = 0.000) for 1448 atoms. Found 7 (7 requested) and removed 12 (3 requested) atoms. Cycle 12: After refmac, R = 0.2275 (Rfree = 0.000) for 1427 atoms. Found 7 (7 requested) and removed 11 (3 requested) atoms. Cycle 13: After refmac, R = 0.2403 (Rfree = 0.000) for 1414 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 14: After refmac, R = 0.2289 (Rfree = 0.000) for 1407 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 15: After refmac, R = 0.2266 (Rfree = 0.000) for 1403 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.74 3.89 Search for helices and strands: 0 residues in 0 chains, 1473 seeds are put forward Round 1: 69 peptides, 16 chains. Longest chain 5 peptides. Score 0.209 Round 2: 83 peptides, 15 chains. Longest chain 10 peptides. Score 0.350 Round 3: 86 peptides, 15 chains. Longest chain 10 peptides. Score 0.371 Round 4: 82 peptides, 15 chains. Longest chain 9 peptides. Score 0.342 Round 5: 80 peptides, 14 chains. Longest chain 10 peptides. Score 0.359 Taking the results from Round 3 Chains 15, Residues 71, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2610 reflections ( 99.58 % complete ) and 3143 restraints for refining 1426 atoms. 2874 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2634 (Rfree = 0.000) for 1426 atoms. Found 7 (7 requested) and removed 11 (3 requested) atoms. Cycle 17: After refmac, R = 0.2451 (Rfree = 0.000) for 1411 atoms. Found 7 (7 requested) and removed 13 (3 requested) atoms. Cycle 18: After refmac, R = 0.2547 (Rfree = 0.000) for 1400 atoms. Found 7 (7 requested) and removed 9 (3 requested) atoms. Cycle 19: After refmac, R = 0.2536 (Rfree = 0.000) for 1391 atoms. Found 7 (7 requested) and removed 9 (3 requested) atoms. Cycle 20: After refmac, R = 0.2414 (Rfree = 0.000) for 1384 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.74 3.89 Search for helices and strands: 0 residues in 0 chains, 1444 seeds are put forward Round 1: 74 peptides, 17 chains. Longest chain 6 peptides. Score 0.216 Round 2: 84 peptides, 17 chains. Longest chain 9 peptides. Score 0.294 Round 3: 94 peptides, 17 chains. Longest chain 9 peptides. Score 0.367 Round 4: 90 peptides, 16 chains. Longest chain 9 peptides. Score 0.369 Round 5: 80 peptides, 14 chains. Longest chain 9 peptides. Score 0.359 Taking the results from Round 4 Chains 16, Residues 74, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2610 reflections ( 99.58 % complete ) and 3266 restraints for refining 1458 atoms. 2986 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2727 (Rfree = 0.000) for 1458 atoms. Found 8 (8 requested) and removed 27 (4 requested) atoms. Cycle 22: After refmac, R = 0.2806 (Rfree = 0.000) for 1435 atoms. Found 7 (7 requested) and removed 13 (3 requested) atoms. Cycle 23: After refmac, R = 0.2599 (Rfree = 0.000) for 1420 atoms. Found 7 (7 requested) and removed 9 (3 requested) atoms. Cycle 24: After refmac, R = 0.2645 (Rfree = 0.000) for 1415 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 25: After refmac, R = 0.2577 (Rfree = 0.000) for 1413 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.67 3.82 Search for helices and strands: 0 residues in 0 chains, 1479 seeds are put forward Round 1: 80 peptides, 18 chains. Longest chain 8 peptides. Score 0.232 Round 2: 98 peptides, 20 chains. Longest chain 10 peptides. Score 0.305 Round 3: 97 peptides, 20 chains. Longest chain 11 peptides. Score 0.298 Round 4: 100 peptides, 17 chains. Longest chain 14 peptides. Score 0.408 Round 5: 97 peptides, 19 chains. Longest chain 8 peptides. Score 0.328 Taking the results from Round 4 Chains 17, Residues 83, Estimated correctness of the model 0.0 % 2 chains (10 residues) have been docked in sequence ------------------------------------------------------ 2610 reflections ( 99.58 % complete ) and 3383 restraints for refining 1537 atoms. 3034 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2651 (Rfree = 0.000) for 1537 atoms. Found 8 (8 requested) and removed 15 (4 requested) atoms. Cycle 27: After refmac, R = 0.2716 (Rfree = 0.000) for 1516 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 28: After refmac, R = 0.2447 (Rfree = 0.000) for 1502 atoms. Found 8 (8 requested) and removed 18 (4 requested) atoms. Cycle 29: After refmac, R = 0.2290 (Rfree = 0.000) for 1485 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 30: After refmac, R = 0.2157 (Rfree = 0.000) for 1476 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.77 3.92 Search for helices and strands: 0 residues in 0 chains, 1552 seeds are put forward Round 1: 54 peptides, 11 chains. Longest chain 8 peptides. Score 0.258 Round 2: 76 peptides, 14 chains. Longest chain 10 peptides. Score 0.330 Round 3: 72 peptides, 13 chains. Longest chain 10 peptides. Score 0.332 Round 4: 77 peptides, 14 chains. Longest chain 10 peptides. Score 0.337 Round 5: 77 peptides, 14 chains. Longest chain 9 peptides. Score 0.337 Taking the results from Round 5 Chains 14, Residues 63, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2610 reflections ( 99.58 % complete ) and 3511 restraints for refining 1504 atoms. 3273 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2695 (Rfree = 0.000) for 1504 atoms. Found 8 (8 requested) and removed 15 (4 requested) atoms. Cycle 32: After refmac, R = 0.2263 (Rfree = 0.000) for 1495 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 33: After refmac, R = 0.2594 (Rfree = 0.000) for 1488 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 34: After refmac, R = 0.2450 (Rfree = 0.000) for 1483 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 35: After refmac, R = 0.2329 (Rfree = 0.000) for 1478 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.79 3.94 Search for helices and strands: 0 residues in 0 chains, 1547 seeds are put forward Round 1: 73 peptides, 16 chains. Longest chain 8 peptides. Score 0.241 Round 2: 78 peptides, 15 chains. Longest chain 7 peptides. Score 0.313 Round 3: 75 peptides, 14 chains. Longest chain 11 peptides. Score 0.322 Round 4: 76 peptides, 14 chains. Longest chain 12 peptides. Score 0.330 Round 5: 71 peptides, 14 chains. Longest chain 8 peptides. Score 0.292 Taking the results from Round 4 Chains 14, Residues 62, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2610 reflections ( 99.58 % complete ) and 3519 restraints for refining 1512 atoms. 3285 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2752 (Rfree = 0.000) for 1512 atoms. Found 8 (8 requested) and removed 17 (4 requested) atoms. Cycle 37: After refmac, R = 0.2646 (Rfree = 0.000) for 1497 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 38: After refmac, R = 0.2489 (Rfree = 0.000) for 1491 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 39: After refmac, R = 0.2694 (Rfree = 0.000) for 1478 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 40: After refmac, R = 0.2309 (Rfree = 0.000) for 1472 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.76 3.91 Search for helices and strands: 0 residues in 0 chains, 1517 seeds are put forward Round 1: 54 peptides, 12 chains. Longest chain 6 peptides. Score 0.221 Round 2: 71 peptides, 13 chains. Longest chain 11 peptides. Score 0.325 Round 3: 68 peptides, 12 chains. Longest chain 9 peptides. Score 0.335 Round 4: 66 peptides, 11 chains. Longest chain 9 peptides. Score 0.353 Round 5: 62 peptides, 10 chains. Longest chain 14 peptides. Score 0.357 Taking the results from Round 5 Chains 10, Residues 52, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2610 reflections ( 99.58 % complete ) and 3324 restraints for refining 1447 atoms. 3126 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2627 (Rfree = 0.000) for 1447 atoms. Found 7 (7 requested) and removed 9 (3 requested) atoms. Cycle 42: After refmac, R = 0.2349 (Rfree = 0.000) for 1441 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 43: After refmac, R = 0.2681 (Rfree = 0.000) for 1431 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 44: After refmac, R = 0.2551 (Rfree = 0.000) for 1423 atoms. Found 7 (7 requested) and removed 13 (3 requested) atoms. Cycle 45: After refmac, R = 0.2431 (Rfree = 0.000) for 1414 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.75 3.90 Search for helices and strands: 0 residues in 0 chains, 1460 seeds are put forward Round 1: 57 peptides, 12 chains. Longest chain 10 peptides. Score 0.247 Round 2: 70 peptides, 14 chains. Longest chain 11 peptides. Score 0.284 Round 3: 75 peptides, 16 chains. Longest chain 7 peptides. Score 0.257 Round 4: 69 peptides, 13 chains. Longest chain 9 peptides. Score 0.309 Round 5: 71 peptides, 14 chains. Longest chain 8 peptides. Score 0.292 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 13, Residues 56, 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 2pg3-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2610 reflections ( 99.58 % complete ) and 3260 restraints for refining 1436 atoms. 3049 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2540 (Rfree = 0.000) for 1436 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.2731 (Rfree = 0.000) for 1425 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.2671 (Rfree = 0.000) for 1420 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.2413 (Rfree = 0.000) for 1412 atoms. TimeTaking 29