null 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 2ifx-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ifx-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ifx-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ifx-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/2ifx-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ifx-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/2ifx-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ifx-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 172 and 0 Target number of residues in the AU: 172 Target solvent content: 0.6494 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-3.6-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: 78 Cell parameters: 46.190 46.190 124.440 90.000 90.000 90.000 Input sequence file: 2ifx-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 0.65 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 3.601 Wilson plot Bfac: 77.07 2994 reflections ( 98.75 % complete ) and 0 restraints for refining 2017 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Starting model: R = 0.3126 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3270 (Rfree = 0.000) for 2017 atoms. Found 12 (12 requested) and removed 19 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.49 3.31 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: 112 peptides, 20 chains. Longest chain 10 peptides. Score 0.383 Round 2: 125 peptides, 14 chains. Longest chain 19 peptides. Score 0.597 Round 3: 134 peptides, 15 chains. Longest chain 19 peptides. Score 0.616 Round 4: 134 peptides, 14 chains. Longest chain 21 peptides. Score 0.636 Round 5: 135 peptides, 14 chains. Longest chain 22 peptides. Score 0.641 Taking the results from Round 5 Chains 14, Residues 121, Estimated correctness of the model 29.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2994 reflections ( 98.75 % complete ) and 3640 restraints for refining 1653 atoms. 3170 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2566 (Rfree = 0.000) for 1653 atoms. Found 7 (10 requested) and removed 14 (5 requested) atoms. Cycle 2: After refmac, R = 0.2533 (Rfree = 0.000) for 1614 atoms. Found 10 (10 requested) and removed 18 (5 requested) atoms. Cycle 3: After refmac, R = 0.2570 (Rfree = 0.000) for 1597 atoms. Found 10 (10 requested) and removed 20 (5 requested) atoms. Cycle 4: After refmac, R = 0.2320 (Rfree = 0.000) for 1584 atoms. Found 9 (10 requested) and removed 16 (5 requested) atoms. Cycle 5: After refmac, R = 0.2058 (Rfree = 0.000) for 1567 atoms. Found 7 (10 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.50 3.32 Search for helices and strands: 0 residues in 0 chains, 1634 seeds are put forward NCS extension: 31 residues added (0 deleted due to clashes), 1665 seeds are put forward Round 1: 119 peptides, 17 chains. Longest chain 13 peptides. Score 0.499 Round 2: 125 peptides, 14 chains. Longest chain 25 peptides. Score 0.597 Round 3: 129 peptides, 16 chains. Longest chain 22 peptides. Score 0.572 Round 4: 142 peptides, 16 chains. Longest chain 16 peptides. Score 0.631 Round 5: 146 peptides, 15 chains. Longest chain 25 peptides. Score 0.666 Taking the results from Round 5 Chains 17, Residues 131, Estimated correctness of the model 38.6 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 2994 reflections ( 98.75 % complete ) and 3439 restraints for refining 1654 atoms. 2891 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2402 (Rfree = 0.000) for 1654 atoms. Found 7 (10 requested) and removed 19 (5 requested) atoms. Cycle 7: After refmac, R = 0.2220 (Rfree = 0.000) for 1639 atoms. Found 6 (10 requested) and removed 19 (5 requested) atoms. Cycle 8: After refmac, R = 0.2319 (Rfree = 0.000) for 1624 atoms. Found 10 (10 requested) and removed 18 (5 requested) atoms. Cycle 9: After refmac, R = 0.2284 (Rfree = 0.000) for 1614 atoms. Found 10 (10 requested) and removed 20 (5 requested) atoms. Cycle 10: After refmac, R = 0.2231 (Rfree = 0.000) for 1602 atoms. Found 10 (10 requested) and removed 23 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.53 3.35 Search for helices and strands: 0 residues in 0 chains, 1654 seeds are put forward NCS extension: 34 residues added (3 deleted due to clashes), 1688 seeds are put forward Round 1: 105 peptides, 15 chains. Longest chain 17 peptides. Score 0.471 Round 2: 120 peptides, 14 chains. Longest chain 15 peptides. Score 0.573 Round 3: 116 peptides, 14 chains. Longest chain 15 peptides. Score 0.553 Round 4: 114 peptides, 13 chains. Longest chain 18 peptides. Score 0.566 Round 5: 124 peptides, 11 chains. Longest chain 27 peptides. Score 0.654 Taking the results from Round 5 Chains 13, Residues 113, Estimated correctness of the model 34.5 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 2994 reflections ( 98.75 % complete ) and 3417 restraints for refining 1654 atoms. 2914 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2382 (Rfree = 0.000) for 1654 atoms. Found 10 (10 requested) and removed 15 (5 requested) atoms. Cycle 12: After refmac, R = 0.2358 (Rfree = 0.000) for 1643 atoms. Found 10 (10 requested) and removed 14 (5 requested) atoms. Cycle 13: After refmac, R = 0.2205 (Rfree = 0.000) for 1635 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Cycle 14: After refmac, R = 0.2159 (Rfree = 0.000) for 1630 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 15: After refmac, R = 0.2208 (Rfree = 0.000) for 1628 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.48 3.30 Search for helices and strands: 0 residues in 0 chains, 1679 seeds are put forward NCS extension: 0 residues added, 1679 seeds are put forward Round 1: 113 peptides, 20 chains. Longest chain 11 peptides. Score 0.389 Round 2: 116 peptides, 17 chains. Longest chain 16 peptides. Score 0.482 Round 3: 128 peptides, 18 chains. Longest chain 13 peptides. Score 0.523 Round 4: 119 peptides, 18 chains. Longest chain 14 peptides. Score 0.475 Round 5: 116 peptides, 17 chains. Longest chain 15 peptides. Score 0.482 Taking the results from Round 3 Chains 18, Residues 110, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2994 reflections ( 98.75 % complete ) and 3789 restraints for refining 1653 atoms. 3367 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2243 (Rfree = 0.000) for 1653 atoms. Found 9 (10 requested) and removed 12 (5 requested) atoms. Cycle 17: After refmac, R = 0.2017 (Rfree = 0.000) for 1647 atoms. Found 9 (10 requested) and removed 7 (5 requested) atoms. Cycle 18: After refmac, R = 0.1830 (Rfree = 0.000) for 1642 atoms. Found 2 (10 requested) and removed 6 (5 requested) atoms. Cycle 19: After refmac, R = 0.1923 (Rfree = 0.000) for 1629 atoms. Found 8 (10 requested) and removed 6 (5 requested) atoms. Cycle 20: After refmac, R = 0.1928 (Rfree = 0.000) for 1629 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.46 3.28 Search for helices and strands: 0 residues in 0 chains, 1662 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 1681 seeds are put forward Round 1: 87 peptides, 19 chains. Longest chain 8 peptides. Score 0.247 Round 2: 103 peptides, 17 chains. Longest chain 11 peptides. Score 0.407 Round 3: 101 peptides, 16 chains. Longest chain 14 peptides. Score 0.422 Round 4: 106 peptides, 19 chains. Longest chain 10 peptides. Score 0.373 Round 5: 109 peptides, 18 chains. Longest chain 12 peptides. Score 0.417 Taking the results from Round 3 Chains 16, Residues 85, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2994 reflections ( 98.75 % complete ) and 3925 restraints for refining 1654 atoms. 3601 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2332 (Rfree = 0.000) for 1654 atoms. Found 10 (10 requested) and removed 56 (5 requested) atoms. Cycle 22: After refmac, R = 0.2247 (Rfree = 0.000) for 1602 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 23: After refmac, R = 0.2284 (Rfree = 0.000) for 1596 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 24: After refmac, R = 0.2206 (Rfree = 0.000) for 1593 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 25: After refmac, R = 0.2153 (Rfree = 0.000) for 1591 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.53 3.35 Search for helices and strands: 0 residues in 0 chains, 1634 seeds are put forward NCS extension: 12 residues added (3 deleted due to clashes), 1646 seeds are put forward Round 1: 85 peptides, 17 chains. Longest chain 8 peptides. Score 0.291 Round 2: 91 peptides, 16 chains. Longest chain 10 peptides. Score 0.360 Round 3: 94 peptides, 16 chains. Longest chain 13 peptides. Score 0.379 Round 4: 96 peptides, 17 chains. Longest chain 10 peptides. Score 0.364 Round 5: 107 peptides, 17 chains. Longest chain 18 peptides. Score 0.431 Taking the results from Round 5 Chains 17, Residues 90, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2994 reflections ( 98.75 % complete ) and 3727 restraints for refining 1654 atoms. 3384 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2208 (Rfree = 0.000) for 1654 atoms. Found 10 (10 requested) and removed 13 (5 requested) atoms. Cycle 27: After refmac, R = 0.2202 (Rfree = 0.000) for 1637 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 28: After refmac, R = 0.2056 (Rfree = 0.000) for 1632 atoms. Found 9 (10 requested) and removed 13 (5 requested) atoms. Cycle 29: After refmac, R = 0.2184 (Rfree = 0.000) for 1623 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 30: After refmac, R = 0.2103 (Rfree = 0.000) for 1618 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.45 3.27 Search for helices and strands: 0 residues in 0 chains, 1671 seeds are put forward NCS extension: 0 residues added, 1671 seeds are put forward Round 1: 78 peptides, 16 chains. Longest chain 7 peptides. Score 0.272 Round 2: 94 peptides, 18 chains. Longest chain 8 peptides. Score 0.323 Round 3: 97 peptides, 19 chains. Longest chain 8 peptides. Score 0.315 Round 4: 94 peptides, 15 chains. Longest chain 15 peptides. Score 0.406 Round 5: 92 peptides, 16 chains. Longest chain 11 peptides. Score 0.366 Taking the results from Round 4 Chains 15, Residues 79, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2994 reflections ( 98.75 % complete ) and 3836 restraints for refining 1651 atoms. 3535 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2538 (Rfree = 0.000) for 1651 atoms. Found 10 (10 requested) and removed 24 (5 requested) atoms. Cycle 32: After refmac, R = 0.1886 (Rfree = 0.000) for 1632 atoms. Found 7 (10 requested) and removed 7 (5 requested) atoms. Cycle 33: After refmac, R = 0.1717 (Rfree = 0.000) for 1631 atoms. Found 2 (10 requested) and removed 7 (5 requested) atoms. Cycle 34: After refmac, R = 0.1598 (Rfree = 0.000) for 1626 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 35: After refmac, R = 0.2254 (Rfree = 0.000) for 1620 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.47 3.29 Search for helices and strands: 0 residues in 0 chains, 1653 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 1672 seeds are put forward Round 1: 79 peptides, 18 chains. Longest chain 6 peptides. Score 0.219 Round 2: 95 peptides, 17 chains. Longest chain 9 peptides. Score 0.357 Round 3: 103 peptides, 19 chains. Longest chain 10 peptides. Score 0.354 Round 4: 104 peptides, 16 chains. Longest chain 13 peptides. Score 0.439 Round 5: 104 peptides, 15 chains. Longest chain 13 peptides. Score 0.465 Taking the results from Round 5 Chains 15, Residues 89, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2994 reflections ( 98.75 % complete ) and 3755 restraints for refining 1654 atoms. 3414 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2185 (Rfree = 0.000) for 1654 atoms. Found 10 (10 requested) and removed 13 (5 requested) atoms. Cycle 37: After refmac, R = 0.2442 (Rfree = 0.000) for 1648 atoms. Found 10 (10 requested) and removed 17 (5 requested) atoms. Cycle 38: After refmac, R = 0.2054 (Rfree = 0.000) for 1635 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 39: After refmac, R = 0.2062 (Rfree = 0.000) for 1633 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. Cycle 40: After refmac, R = 0.1934 (Rfree = 0.000) for 1636 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.47 3.29 Search for helices and strands: 0 residues in 0 chains, 1671 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 1692 seeds are put forward Round 1: 80 peptides, 17 chains. Longest chain 7 peptides. Score 0.256 Round 2: 84 peptides, 15 chains. Longest chain 9 peptides. Score 0.342 Round 3: 86 peptides, 15 chains. Longest chain 8 peptides. Score 0.355 Round 4: 95 peptides, 15 chains. Longest chain 11 peptides. Score 0.412 Round 5: 98 peptides, 15 chains. Longest chain 13 peptides. Score 0.430 Taking the results from Round 5 Chains 15, Residues 83, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2994 reflections ( 98.75 % complete ) and 3797 restraints for refining 1654 atoms. 3480 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2196 (Rfree = 0.000) for 1654 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. Cycle 42: After refmac, R = 0.1990 (Rfree = 0.000) for 1656 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. Cycle 43: After refmac, R = 0.2239 (Rfree = 0.000) for 1657 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 44: After refmac, R = 0.1909 (Rfree = 0.000) for 1652 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 45: After refmac, R = 0.2171 (Rfree = 0.000) for 1649 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.48 3.30 Search for helices and strands: 0 residues in 0 chains, 1696 seeds are put forward NCS extension: 0 residues added, 1696 seeds are put forward Round 1: 67 peptides, 14 chains. Longest chain 7 peptides. Score 0.253 Round 2: 79 peptides, 15 chains. Longest chain 9 peptides. Score 0.308 Round 3: 83 peptides, 14 chains. Longest chain 13 peptides. Score 0.364 Round 4: 82 peptides, 15 chains. Longest chain 9 peptides. Score 0.329 Round 5: 78 peptides, 15 chains. Longest chain 8 peptides. Score 0.302 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 14, Residues 69, 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. 2994 reflections ( 98.75 % complete ) and 3894 restraints for refining 1654 atoms. 3632 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2211 (Rfree = 0.000) for 1654 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2236 (Rfree = 0.000) for 1646 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2021 (Rfree = 0.000) for 1636 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.2285 (Rfree = 0.000) for 1631 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:53:28 GMT 2018 Job finished. TimeTaking 30.38 Used memory is bytes: 4337480