Sun 23 Dec 22:23:10 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-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ifx-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ifx-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ifx-3.2-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-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ifx-3.2-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 22:23:18 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-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ifx-3.2-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 180 and 0 Target number of residues in the AU: 180 Target solvent content: 0.6331 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-3.2-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-3.2-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 3.201 Wilson plot Bfac: 67.97 4280 reflections ( 99.07 % complete ) and 0 restraints for refining 2011 atoms. Observations/parameters ratio is 0.53 ------------------------------------------------------ Starting model: R = 0.3129 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2462 (Rfree = 0.000) for 2011 atoms. Found 6 (18 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.22 3.05 Search for helices and strands: 0 residues in 0 chains, 2043 seeds are put forward NCS extension: 0 residues added, 2043 seeds are put forward Round 1: 115 peptides, 18 chains. Longest chain 14 peptides. Score 0.452 Round 2: 136 peptides, 18 chains. Longest chain 16 peptides. Score 0.563 Round 3: 145 peptides, 20 chains. Longest chain 15 peptides. Score 0.563 Round 4: 155 peptides, 15 chains. Longest chain 20 peptides. Score 0.700 Round 5: 162 peptides, 17 chains. Longest chain 20 peptides. Score 0.691 Taking the results from Round 4 Chains 15, Residues 140, Estimated correctness of the model 65.1 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 4280 reflections ( 99.07 % complete ) and 3346 restraints for refining 1665 atoms. 2748 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2709 (Rfree = 0.000) for 1665 atoms. Found 13 (14 requested) and removed 21 (7 requested) atoms. Cycle 2: After refmac, R = 0.2617 (Rfree = 0.000) for 1626 atoms. Found 6 (14 requested) and removed 19 (7 requested) atoms. Cycle 3: After refmac, R = 0.2489 (Rfree = 0.000) for 1595 atoms. Found 8 (14 requested) and removed 10 (7 requested) atoms. Cycle 4: After refmac, R = 0.2386 (Rfree = 0.000) for 1586 atoms. Found 6 (14 requested) and removed 8 (7 requested) atoms. Cycle 5: After refmac, R = 0.2308 (Rfree = 0.000) for 1575 atoms. Found 3 (14 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.22 3.05 Search for helices and strands: 0 residues in 0 chains, 1629 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 1647 seeds are put forward Round 1: 146 peptides, 20 chains. Longest chain 19 peptides. Score 0.568 Round 2: 153 peptides, 19 chains. Longest chain 16 peptides. Score 0.620 Round 3: 149 peptides, 16 chains. Longest chain 19 peptides. Score 0.660 Round 4: 151 peptides, 16 chains. Longest chain 21 peptides. Score 0.667 Round 5: 150 peptides, 18 chains. Longest chain 15 peptides. Score 0.626 Taking the results from Round 4 Chains 17, Residues 135, Estimated correctness of the model 57.8 % 3 chains (26 residues) have been docked in sequence ------------------------------------------------------ 4280 reflections ( 99.07 % complete ) and 3425 restraints for refining 1655 atoms. 2799 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2971 (Rfree = 0.000) for 1655 atoms. Found 14 (14 requested) and removed 31 (7 requested) atoms. Cycle 7: After refmac, R = 0.2943 (Rfree = 0.000) for 1623 atoms. Found 14 (14 requested) and removed 36 (7 requested) atoms. Cycle 8: After refmac, R = 0.2999 (Rfree = 0.000) for 1587 atoms. Found 14 (14 requested) and removed 22 (7 requested) atoms. Cycle 9: After refmac, R = 0.2518 (Rfree = 0.000) for 1565 atoms. Found 14 (14 requested) and removed 18 (7 requested) atoms. Cycle 10: After refmac, R = 0.3020 (Rfree = 0.000) for 1558 atoms. Found 13 (13 requested) and removed 22 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.12 2.96 Search for helices and strands: 0 residues in 0 chains, 1630 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 1654 seeds are put forward Round 1: 133 peptides, 19 chains. Longest chain 17 peptides. Score 0.526 Round 2: 153 peptides, 21 chains. Longest chain 15 peptides. Score 0.580 Round 3: 140 peptides, 17 chains. Longest chain 17 peptides. Score 0.602 Round 4: 140 peptides, 20 chains. Longest chain 15 peptides. Score 0.539 Round 5: 135 peptides, 19 chains. Longest chain 15 peptides. Score 0.536 Taking the results from Round 3 Chains 18, Residues 123, Estimated correctness of the model 41.5 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 4280 reflections ( 99.07 % complete ) and 3362 restraints for refining 1622 atoms. 2824 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3120 (Rfree = 0.000) for 1622 atoms. Found 14 (14 requested) and removed 40 (7 requested) atoms. Cycle 12: After refmac, R = 0.2620 (Rfree = 0.000) for 1584 atoms. Found 10 (14 requested) and removed 19 (7 requested) atoms. Cycle 13: After refmac, R = 0.2787 (Rfree = 0.000) for 1567 atoms. Found 11 (14 requested) and removed 18 (7 requested) atoms. Cycle 14: After refmac, R = 0.2472 (Rfree = 0.000) for 1557 atoms. Found 11 (13 requested) and removed 11 (6 requested) atoms. Cycle 15: After refmac, R = 0.2945 (Rfree = 0.000) for 1553 atoms. Found 13 (13 requested) and removed 27 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.23 3.06 Search for helices and strands: 0 residues in 0 chains, 1588 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 1602 seeds are put forward Round 1: 118 peptides, 20 chains. Longest chain 15 peptides. Score 0.419 Round 2: 131 peptides, 17 chains. Longest chain 15 peptides. Score 0.560 Round 3: 129 peptides, 18 chains. Longest chain 16 peptides. Score 0.528 Round 4: 140 peptides, 18 chains. Longest chain 17 peptides. Score 0.582 Round 5: 146 peptides, 19 chains. Longest chain 18 peptides. Score 0.589 Taking the results from Round 5 Chains 19, Residues 127, Estimated correctness of the model 38.0 % 1 chains (17 residues) have been docked in sequence ------------------------------------------------------ 4280 reflections ( 99.07 % complete ) and 3408 restraints for refining 1665 atoms. 2833 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2869 (Rfree = 0.000) for 1665 atoms. Found 10 (14 requested) and removed 22 (7 requested) atoms. Cycle 17: After refmac, R = 0.2968 (Rfree = 0.000) for 1644 atoms. Found 14 (14 requested) and removed 24 (7 requested) atoms. Cycle 18: After refmac, R = 0.2563 (Rfree = 0.000) for 1626 atoms. Found 10 (14 requested) and removed 10 (7 requested) atoms. Cycle 19: After refmac, R = 0.2884 (Rfree = 0.000) for 1619 atoms. Found 14 (14 requested) and removed 23 (7 requested) atoms. Cycle 20: After refmac, R = 0.2448 (Rfree = 0.000) for 1605 atoms. Found 12 (14 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.19 3.02 Search for helices and strands: 0 residues in 0 chains, 1665 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 1687 seeds are put forward Round 1: 128 peptides, 23 chains. Longest chain 14 peptides. Score 0.403 Round 2: 148 peptides, 19 chains. Longest chain 19 peptides. Score 0.598 Round 3: 150 peptides, 24 chains. Longest chain 13 peptides. Score 0.501 Round 4: 137 peptides, 19 chains. Longest chain 15 peptides. Score 0.546 Round 5: 148 peptides, 20 chains. Longest chain 19 peptides. Score 0.577 Taking the results from Round 2 Chains 21, Residues 129, Estimated correctness of the model 40.5 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 4280 reflections ( 99.07 % complete ) and 3431 restraints for refining 1665 atoms. 2877 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2486 (Rfree = 0.000) for 1665 atoms. Found 14 (14 requested) and removed 23 (7 requested) atoms. Cycle 22: After refmac, R = 0.2526 (Rfree = 0.000) for 1653 atoms. Found 14 (14 requested) and removed 15 (7 requested) atoms. Cycle 23: After refmac, R = 0.2948 (Rfree = 0.000) for 1649 atoms. Found 14 (14 requested) and removed 19 (7 requested) atoms. Cycle 24: After refmac, R = 0.2117 (Rfree = 0.000) for 1630 atoms. Found 8 (14 requested) and removed 11 (7 requested) atoms. Cycle 25: After refmac, R = 0.2204 (Rfree = 0.000) for 1621 atoms. Found 14 (14 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.20 3.03 Search for helices and strands: 0 residues in 0 chains, 1699 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 1718 seeds are put forward Round 1: 113 peptides, 19 chains. Longest chain 15 peptides. Score 0.415 Round 2: 140 peptides, 19 chains. Longest chain 19 peptides. Score 0.560 Round 3: 153 peptides, 19 chains. Longest chain 20 peptides. Score 0.620 Round 4: 154 peptides, 21 chains. Longest chain 16 peptides. Score 0.584 Round 5: 154 peptides, 16 chains. Longest chain 20 peptides. Score 0.679 Taking the results from Round 5 Chains 17, Residues 138, Estimated correctness of the model 60.6 % 3 chains (34 residues) have been docked in sequence ------------------------------------------------------ 4280 reflections ( 99.07 % complete ) and 3012 restraints for refining 1665 atoms. 2340 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3055 (Rfree = 0.000) for 1665 atoms. Found 14 (14 requested) and removed 30 (7 requested) atoms. Cycle 27: After refmac, R = 0.2795 (Rfree = 0.000) for 1632 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 28: After refmac, R = 0.2706 (Rfree = 0.000) for 1618 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 29: After refmac, R = 0.2195 (Rfree = 0.000) for 1614 atoms. Found 6 (14 requested) and removed 12 (7 requested) atoms. Cycle 30: After refmac, R = 0.2580 (Rfree = 0.000) for 1606 atoms. Found 14 (14 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.17 3.01 Search for helices and strands: 0 residues in 0 chains, 1658 seeds are put forward NCS extension: 19 residues added (3 deleted due to clashes), 1677 seeds are put forward Round 1: 124 peptides, 21 chains. Longest chain 12 peptides. Score 0.429 Round 2: 125 peptides, 19 chains. Longest chain 13 peptides. Score 0.483 Round 3: 122 peptides, 17 chains. Longest chain 16 peptides. Score 0.515 Round 4: 133 peptides, 18 chains. Longest chain 17 peptides. Score 0.548 Round 5: 135 peptides, 16 chains. Longest chain 19 peptides. Score 0.600 Taking the results from Round 5 Chains 18, Residues 119, Estimated correctness of the model 41.0 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 4280 reflections ( 99.07 % complete ) and 3429 restraints for refining 1665 atoms. 2912 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2276 (Rfree = 0.000) for 1665 atoms. Found 13 (14 requested) and removed 12 (7 requested) atoms. Cycle 32: After refmac, R = 0.2165 (Rfree = 0.000) for 1659 atoms. Found 5 (14 requested) and removed 9 (7 requested) atoms. Cycle 33: After refmac, R = 0.1969 (Rfree = 0.000) for 1652 atoms. Found 2 (14 requested) and removed 8 (7 requested) atoms. Cycle 34: After refmac, R = 0.1900 (Rfree = 0.000) for 1637 atoms. Found 3 (14 requested) and removed 7 (7 requested) atoms. Cycle 35: After refmac, R = 0.1921 (Rfree = 0.000) for 1633 atoms. Found 5 (14 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.22 3.05 Search for helices and strands: 0 residues in 0 chains, 1677 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 1694 seeds are put forward Round 1: 113 peptides, 22 chains. Longest chain 10 peptides. Score 0.337 Round 2: 127 peptides, 21 chains. Longest chain 12 peptides. Score 0.446 Round 3: 121 peptides, 18 chains. Longest chain 18 peptides. Score 0.486 Round 4: 123 peptides, 21 chains. Longest chain 10 peptides. Score 0.423 Round 5: 130 peptides, 20 chains. Longest chain 14 peptides. Score 0.487 Taking the results from Round 5 Chains 20, Residues 110, Estimated correctness of the model 7.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4280 reflections ( 99.07 % complete ) and 3691 restraints for refining 1665 atoms. 3271 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2248 (Rfree = 0.000) for 1665 atoms. Found 14 (14 requested) and removed 10 (7 requested) atoms. Cycle 37: After refmac, R = 0.2154 (Rfree = 0.000) for 1665 atoms. Found 9 (14 requested) and removed 8 (7 requested) atoms. Cycle 38: After refmac, R = 0.2023 (Rfree = 0.000) for 1662 atoms. Found 2 (14 requested) and removed 11 (7 requested) atoms. Cycle 39: After refmac, R = 0.2061 (Rfree = 0.000) for 1649 atoms. Found 8 (14 requested) and removed 10 (7 requested) atoms. Cycle 40: After refmac, R = 0.2023 (Rfree = 0.000) for 1642 atoms. Found 6 (14 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.24 3.07 Search for helices and strands: 0 residues in 0 chains, 1692 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 1711 seeds are put forward Round 1: 101 peptides, 21 chains. Longest chain 8 peptides. Score 0.286 Round 2: 118 peptides, 22 chains. Longest chain 11 peptides. Score 0.368 Round 3: 120 peptides, 22 chains. Longest chain 12 peptides. Score 0.380 Round 4: 127 peptides, 21 chains. Longest chain 12 peptides. Score 0.446 Round 5: 130 peptides, 21 chains. Longest chain 14 peptides. Score 0.463 Taking the results from Round 5 Chains 21, Residues 109, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4280 reflections ( 99.07 % complete ) and 3736 restraints for refining 1665 atoms. 3321 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3015 (Rfree = 0.000) for 1665 atoms. Found 14 (14 requested) and removed 17 (7 requested) atoms. Cycle 42: After refmac, R = 0.2463 (Rfree = 0.000) for 1651 atoms. Found 14 (14 requested) and removed 11 (7 requested) atoms. Cycle 43: After refmac, R = 0.2009 (Rfree = 0.000) for 1652 atoms. Found 6 (14 requested) and removed 8 (7 requested) atoms. Cycle 44: After refmac, R = 0.1863 (Rfree = 0.000) for 1650 atoms. Found 7 (14 requested) and removed 8 (7 requested) atoms. Cycle 45: After refmac, R = 0.2045 (Rfree = 0.000) for 1648 atoms. Found 14 (14 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.25 3.08 Search for helices and strands: 0 residues in 0 chains, 1688 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 1705 seeds are put forward Round 1: 104 peptides, 20 chains. Longest chain 10 peptides. Score 0.333 Round 2: 116 peptides, 21 chains. Longest chain 10 peptides. Score 0.382 Round 3: 114 peptides, 19 chains. Longest chain 11 peptides. Score 0.421 Round 4: 118 peptides, 18 chains. Longest chain 12 peptides. Score 0.469 Round 5: 128 peptides, 21 chains. Longest chain 10 peptides. Score 0.452 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 18, Residues 100, Estimated correctness of the model 0.9 % 1 chains (6 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 2ifx-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4280 reflections ( 99.07 % complete ) and 3544 restraints for refining 1665 atoms. 3146 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2244 (Rfree = 0.000) for 1665 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.2271 (Rfree = 0.000) for 1657 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.1987 (Rfree = 0.000) for 1648 atoms. Found 0 (14 requested) and removed 1 (7 requested) atoms. Cycle 49: After refmac, R = 0.1916 (Rfree = 0.000) for 1645 atoms. TimeTaking 31.53