null Sun 23 Dec 22:22:49 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 2ifx-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ifx-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ifx-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ifx-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/2ifx-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ifx-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 22:22:59 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/2ifx-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ifx-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 169 and 0 Target number of residues in the AU: 169 Target solvent content: 0.6555 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: 0.54 Input MTZ file: 2ifx-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: 78 Cell parameters: 46.190 46.190 124.440 90.000 90.000 90.000 Input sequence file: 2ifx-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 1824 target number of atoms Had to go as low as 0.65 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: 28.919 3.800 Wilson plot Bfac: 80.87 2547 reflections ( 98.61 % complete ) and 0 restraints for refining 2025 atoms. Observations/parameters ratio is 0.31 ------------------------------------------------------ Starting model: R = 0.3193 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3223 (Rfree = 0.000) for 2025 atoms. Found 11 (11 requested) and removed 21 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.68 3.49 Search for helices and strands: 0 residues in 0 chains, 2049 seeds are put forward NCS extension: 0 residues added, 2049 seeds are put forward Round 1: 91 peptides, 18 chains. Longest chain 8 peptides. Score 0.303 Round 2: 116 peptides, 17 chains. Longest chain 16 peptides. Score 0.482 Round 3: 131 peptides, 14 chains. Longest chain 16 peptides. Score 0.624 Round 4: 124 peptides, 14 chains. Longest chain 17 peptides. Score 0.592 Round 5: 120 peptides, 13 chains. Longest chain 20 peptides. Score 0.595 Taking the results from Round 3 Chains 16, Residues 117, Estimated correctness of the model 9.7 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 2547 reflections ( 98.61 % complete ) and 3629 restraints for refining 1649 atoms. 3151 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2647 (Rfree = 0.000) for 1649 atoms. Found 9 (9 requested) and removed 20 (4 requested) atoms. Cycle 2: After refmac, R = 0.2996 (Rfree = 0.000) for 1614 atoms. Found 9 (9 requested) and removed 23 (4 requested) atoms. Cycle 3: After refmac, R = 0.2574 (Rfree = 0.000) for 1590 atoms. Found 8 (8 requested) and removed 14 (4 requested) atoms. Cycle 4: After refmac, R = 0.2420 (Rfree = 0.000) for 1567 atoms. Found 8 (8 requested) and removed 15 (4 requested) atoms. Cycle 5: After refmac, R = 0.2485 (Rfree = 0.000) for 1551 atoms. Found 8 (8 requested) and removed 14 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.65 3.46 Search for helices and strands: 0 residues in 0 chains, 1621 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 1634 seeds are put forward Round 1: 101 peptides, 15 chains. Longest chain 13 peptides. Score 0.448 Round 2: 110 peptides, 17 chains. Longest chain 17 peptides. Score 0.449 Round 3: 126 peptides, 19 chains. Longest chain 14 peptides. Score 0.489 Round 4: 114 peptides, 13 chains. Longest chain 21 peptides. Score 0.566 Round 5: 120 peptides, 15 chains. Longest chain 18 peptides. Score 0.551 Taking the results from Round 4 Chains 13, Residues 101, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2547 reflections ( 98.61 % complete ) and 3571 restraints for refining 1578 atoms. 3180 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2693 (Rfree = 0.000) for 1578 atoms. Found 8 (8 requested) and removed 16 (4 requested) atoms. Cycle 7: After refmac, R = 0.2537 (Rfree = 0.000) for 1558 atoms. Found 8 (8 requested) and removed 24 (4 requested) atoms. Cycle 8: After refmac, R = 0.2454 (Rfree = 0.000) for 1536 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. Cycle 9: After refmac, R = 0.2370 (Rfree = 0.000) for 1525 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 10: After refmac, R = 0.2169 (Rfree = 0.000) for 1517 atoms. Found 8 (8 requested) and removed 14 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.58 3.39 Search for helices and strands: 0 residues in 0 chains, 1563 seeds are put forward NCS extension: 35 residues added (1 deleted due to clashes), 1598 seeds are put forward Round 1: 108 peptides, 18 chains. Longest chain 10 peptides. Score 0.411 Round 2: 129 peptides, 18 chains. Longest chain 18 peptides. Score 0.528 Round 3: 130 peptides, 18 chains. Longest chain 12 peptides. Score 0.533 Round 4: 134 peptides, 17 chains. Longest chain 15 peptides. Score 0.575 Round 5: 135 peptides, 18 chains. Longest chain 16 peptides. Score 0.558 Taking the results from Round 4 Chains 17, Residues 117, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2547 reflections ( 98.61 % complete ) and 3333 restraints for refining 1555 atoms. 2882 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2095 (Rfree = 0.000) for 1555 atoms. Found 5 (8 requested) and removed 18 (4 requested) atoms. Cycle 12: After refmac, R = 0.2334 (Rfree = 0.000) for 1530 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 13: After refmac, R = 0.2200 (Rfree = 0.000) for 1512 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 14: After refmac, R = 0.2148 (Rfree = 0.000) for 1502 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 15: After refmac, R = 0.2052 (Rfree = 0.000) for 1498 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.68 3.49 Search for helices and strands: 0 residues in 0 chains, 1548 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 1551 seeds are put forward Round 1: 91 peptides, 18 chains. Longest chain 9 peptides. Score 0.303 Round 2: 100 peptides, 17 chains. Longest chain 9 peptides. Score 0.389 Round 3: 103 peptides, 18 chains. Longest chain 9 peptides. Score 0.381 Round 4: 107 peptides, 17 chains. Longest chain 15 peptides. Score 0.431 Round 5: 117 peptides, 17 chains. Longest chain 21 peptides. Score 0.488 Taking the results from Round 5 Chains 17, Residues 100, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 2547 reflections ( 98.61 % complete ) and 3627 restraints for refining 1605 atoms. 3227 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2420 (Rfree = 0.000) for 1605 atoms. Found 8 (8 requested) and removed 17 (4 requested) atoms. Cycle 17: After refmac, R = 0.2247 (Rfree = 0.000) for 1573 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 18: After refmac, R = 0.2158 (Rfree = 0.000) for 1557 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 19: After refmac, R = 0.2675 (Rfree = 0.000) for 1542 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 20: After refmac, R = 0.2039 (Rfree = 0.000) for 1523 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.62 3.43 Search for helices and strands: 0 residues in 0 chains, 1605 seeds are put forward NCS extension: 0 residues added, 1605 seeds are put forward Round 1: 78 peptides, 17 chains. Longest chain 7 peptides. Score 0.242 Round 2: 109 peptides, 17 chains. Longest chain 15 peptides. Score 0.443 Round 3: 94 peptides, 18 chains. Longest chain 9 peptides. Score 0.323 Round 4: 93 peptides, 16 chains. Longest chain 9 peptides. Score 0.372 Round 5: 99 peptides, 18 chains. Longest chain 9 peptides. Score 0.356 Taking the results from Round 2 Chains 17, Residues 92, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2547 reflections ( 98.61 % complete ) and 3297 restraints for refining 1502 atoms. 2946 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2102 (Rfree = 0.000) for 1502 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 22: After refmac, R = 0.1958 (Rfree = 0.000) for 1485 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 23: After refmac, R = 0.2242 (Rfree = 0.000) for 1467 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 24: After refmac, R = 0.2045 (Rfree = 0.000) for 1456 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 25: After refmac, R = 0.2064 (Rfree = 0.000) for 1451 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.54 3.36 Search for helices and strands: 0 residues in 0 chains, 1525 seeds are put forward NCS extension: 0 residues added, 1525 seeds are put forward Round 1: 92 peptides, 18 chains. Longest chain 10 peptides. Score 0.310 Round 2: 109 peptides, 17 chains. Longest chain 12 peptides. Score 0.443 Round 3: 99 peptides, 16 chains. Longest chain 12 peptides. Score 0.410 Round 4: 101 peptides, 16 chains. Longest chain 10 peptides. Score 0.422 Round 5: 105 peptides, 17 chains. Longest chain 11 peptides. Score 0.419 Taking the results from Round 2 Chains 17, Residues 92, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2547 reflections ( 98.61 % complete ) and 3414 restraints for refining 1534 atoms. 3063 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2253 (Rfree = 0.000) for 1534 atoms. Found 8 (8 requested) and removed 19 (4 requested) atoms. Cycle 27: After refmac, R = 0.2146 (Rfree = 0.000) for 1509 atoms. Found 6 (8 requested) and removed 9 (4 requested) atoms. Cycle 28: After refmac, R = 0.1957 (Rfree = 0.000) for 1495 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 29: After refmac, R = 0.2255 (Rfree = 0.000) for 1485 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 30: After refmac, R = 0.1890 (Rfree = 0.000) for 1478 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.64 3.45 Search for helices and strands: 0 residues in 0 chains, 1541 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 1557 seeds are put forward Round 1: 77 peptides, 15 chains. Longest chain 9 peptides. Score 0.295 Round 2: 109 peptides, 22 chains. Longest chain 8 peptides. Score 0.311 Round 3: 92 peptides, 16 chains. Longest chain 10 peptides. Score 0.366 Round 4: 95 peptides, 18 chains. Longest chain 9 peptides. Score 0.330 Round 5: 96 peptides, 16 chains. Longest chain 10 peptides. Score 0.391 Taking the results from Round 5 Chains 16, Residues 80, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2547 reflections ( 98.61 % complete ) and 3587 restraints for refining 1579 atoms. 3283 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2159 (Rfree = 0.000) for 1579 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 32: After refmac, R = 0.2328 (Rfree = 0.000) for 1565 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 33: After refmac, R = 0.2304 (Rfree = 0.000) for 1556 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 34: After refmac, R = 0.2296 (Rfree = 0.000) for 1548 atoms. Found 8 (8 requested) and removed 14 (4 requested) atoms. Cycle 35: After refmac, R = 0.1895 (Rfree = 0.000) for 1539 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.65 3.46 Search for helices and strands: 0 residues in 0 chains, 1603 seeds are put forward NCS extension: 9 residues added (0 deleted due to clashes), 1612 seeds are put forward Round 1: 75 peptides, 17 chains. Longest chain 6 peptides. Score 0.220 Round 2: 91 peptides, 16 chains. Longest chain 10 peptides. Score 0.360 Round 3: 92 peptides, 15 chains. Longest chain 11 peptides. Score 0.394 Round 4: 82 peptides, 12 chains. Longest chain 10 peptides. Score 0.415 Round 5: 88 peptides, 13 chains. Longest chain 10 peptides. Score 0.424 Taking the results from Round 5 Chains 13, Residues 75, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2547 reflections ( 98.61 % complete ) and 3828 restraints for refining 1644 atoms. 3541 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2300 (Rfree = 0.000) for 1644 atoms. Found 9 (9 requested) and removed 20 (4 requested) atoms. Cycle 37: After refmac, R = 0.2154 (Rfree = 0.000) for 1620 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 38: After refmac, R = 0.2202 (Rfree = 0.000) for 1605 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. Cycle 39: After refmac, R = 0.2345 (Rfree = 0.000) for 1594 atoms. Found 8 (8 requested) and removed 21 (4 requested) atoms. Cycle 40: After refmac, R = 0.2012 (Rfree = 0.000) for 1575 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.57 3.38 Search for helices and strands: 0 residues in 0 chains, 1643 seeds are put forward NCS extension: 0 residues added, 1643 seeds are put forward Round 1: 72 peptides, 16 chains. Longest chain 6 peptides. Score 0.228 Round 2: 93 peptides, 18 chains. Longest chain 10 peptides. Score 0.317 Round 3: 98 peptides, 19 chains. Longest chain 9 peptides. Score 0.322 Round 4: 88 peptides, 17 chains. Longest chain 11 peptides. Score 0.312 Round 5: 92 peptides, 18 chains. Longest chain 8 peptides. Score 0.310 Taking the results from Round 3 Chains 19, Residues 79, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 2547 reflections ( 98.61 % complete ) and 3477 restraints for refining 1566 atoms. 3160 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2015 (Rfree = 0.000) for 1566 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. Cycle 42: After refmac, R = 0.1848 (Rfree = 0.000) for 1553 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 43: After refmac, R = 0.2206 (Rfree = 0.000) for 1545 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 44: After refmac, R = 0.2027 (Rfree = 0.000) for 1535 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 45: After refmac, R = 0.2047 (Rfree = 0.000) for 1530 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.62 3.43 Search for helices and strands: 0 residues in 0 chains, 1577 seeds are put forward NCS extension: 0 residues added, 1577 seeds are put forward Round 1: 71 peptides, 15 chains. Longest chain 7 peptides. Score 0.252 Round 2: 94 peptides, 18 chains. Longest chain 8 peptides. Score 0.323 Round 3: 77 peptides, 14 chains. Longest chain 7 peptides. Score 0.324 Round 4: 78 peptides, 14 chains. Longest chain 8 peptides. Score 0.331 Round 5: 81 peptides, 14 chains. Longest chain 9 peptides. Score 0.351 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 14, Residues 67, 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 2ifx-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2547 reflections ( 98.61 % complete ) and 3698 restraints for refining 1608 atoms. 3444 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2526 (Rfree = 0.000) for 1608 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2148 (Rfree = 0.000) for 1597 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.1898 (Rfree = 0.000) for 1591 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.2096 (Rfree = 0.000) for 1584 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:52:28 GMT 2018 Job finished. TimeTaking 29.64 Used memory is bytes: 20431504