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-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ifx-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ifx-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ifx-3.4-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-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ifx-3.4-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 22:22:58 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-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ifx-3.4-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 176 and 0 Target number of residues in the AU: 176 Target solvent content: 0.6412 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-3.4-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-3.4-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 3.401 Wilson plot Bfac: 72.01 3571 reflections ( 98.92 % complete ) and 0 restraints for refining 2023 atoms. Observations/parameters ratio is 0.44 ------------------------------------------------------ Starting model: R = 0.3080 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3040 (Rfree = 0.000) for 2023 atoms. Found 15 (15 requested) and removed 22 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.34 3.17 Search for helices and strands: 0 residues in 0 chains, 2044 seeds are put forward NCS extension: 0 residues added, 2044 seeds are put forward Round 1: 101 peptides, 19 chains. Longest chain 10 peptides. Score 0.341 Round 2: 134 peptides, 19 chains. Longest chain 14 peptides. Score 0.531 Round 3: 145 peptides, 20 chains. Longest chain 15 peptides. Score 0.563 Round 4: 147 peptides, 16 chains. Longest chain 20 peptides. Score 0.652 Round 5: 138 peptides, 15 chains. Longest chain 20 peptides. Score 0.634 Taking the results from Round 4 Chains 20, Residues 131, Estimated correctness of the model 44.7 % 3 chains (39 residues) have been docked in sequence ------------------------------------------------------ 3571 reflections ( 98.92 % complete ) and 3206 restraints for refining 1658 atoms. 2539 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2852 (Rfree = 0.000) for 1658 atoms. Found 12 (12 requested) and removed 25 (6 requested) atoms. Cycle 2: After refmac, R = 0.2586 (Rfree = 0.000) for 1603 atoms. Found 7 (12 requested) and removed 13 (6 requested) atoms. Cycle 3: After refmac, R = 0.2756 (Rfree = 0.000) for 1580 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 4: After refmac, R = 0.2427 (Rfree = 0.000) for 1571 atoms. Found 7 (11 requested) and removed 8 (5 requested) atoms. Cycle 5: After refmac, R = 0.2412 (Rfree = 0.000) for 1566 atoms. Found 6 (11 requested) and removed 15 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.34 3.17 Search for helices and strands: 0 residues in 0 chains, 1623 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 1642 seeds are put forward Round 1: 129 peptides, 21 chains. Longest chain 18 peptides. Score 0.458 Round 2: 137 peptides, 18 chains. Longest chain 19 peptides. Score 0.567 Round 3: 143 peptides, 18 chains. Longest chain 18 peptides. Score 0.595 Round 4: 142 peptides, 19 chains. Longest chain 17 peptides. Score 0.570 Round 5: 142 peptides, 16 chains. Longest chain 18 peptides. Score 0.631 Taking the results from Round 5 Chains 16, Residues 126, Estimated correctness of the model 38.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3571 reflections ( 98.92 % complete ) and 3650 restraints for refining 1658 atoms. 3162 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2348 (Rfree = 0.000) for 1658 atoms. Found 9 (12 requested) and removed 18 (6 requested) atoms. Cycle 7: After refmac, R = 0.2129 (Rfree = 0.000) for 1641 atoms. Found 5 (12 requested) and removed 13 (6 requested) atoms. Cycle 8: After refmac, R = 0.1989 (Rfree = 0.000) for 1628 atoms. Found 4 (12 requested) and removed 11 (6 requested) atoms. Cycle 9: After refmac, R = 0.1992 (Rfree = 0.000) for 1620 atoms. Found 5 (12 requested) and removed 8 (6 requested) atoms. Cycle 10: After refmac, R = 0.1999 (Rfree = 0.000) for 1611 atoms. Found 7 (12 requested) and removed 13 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.31 3.14 Search for helices and strands: 0 residues in 0 chains, 1664 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 1683 seeds are put forward Round 1: 123 peptides, 21 chains. Longest chain 13 peptides. Score 0.423 Round 2: 129 peptides, 18 chains. Longest chain 16 peptides. Score 0.528 Round 3: 137 peptides, 18 chains. Longest chain 16 peptides. Score 0.567 Round 4: 137 peptides, 18 chains. Longest chain 15 peptides. Score 0.567 Round 5: 141 peptides, 21 chains. Longest chain 18 peptides. Score 0.522 Taking the results from Round 4 Chains 18, Residues 119, Estimated correctness of the model 17.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3571 reflections ( 98.92 % complete ) and 3672 restraints for refining 1658 atoms. 3214 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2189 (Rfree = 0.000) for 1658 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 12: After refmac, R = 0.1987 (Rfree = 0.000) for 1643 atoms. Found 5 (12 requested) and removed 10 (6 requested) atoms. Cycle 13: After refmac, R = 0.2167 (Rfree = 0.000) for 1637 atoms. Found 6 (12 requested) and removed 15 (6 requested) atoms. Cycle 14: After refmac, R = 0.2270 (Rfree = 0.000) for 1623 atoms. Found 10 (12 requested) and removed 8 (6 requested) atoms. Cycle 15: After refmac, R = 0.2148 (Rfree = 0.000) for 1621 atoms. Found 7 (12 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.34 3.17 Search for helices and strands: 0 residues in 0 chains, 1689 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 1704 seeds are put forward Round 1: 125 peptides, 24 chains. Longest chain 12 peptides. Score 0.359 Round 2: 143 peptides, 20 chains. Longest chain 19 peptides. Score 0.553 Round 3: 141 peptides, 22 chains. Longest chain 19 peptides. Score 0.499 Round 4: 135 peptides, 18 chains. Longest chain 16 peptides. Score 0.558 Round 5: 124 peptides, 17 chains. Longest chain 13 peptides. Score 0.525 Taking the results from Round 4 Chains 18, Residues 117, Estimated correctness of the model 14.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3571 reflections ( 98.92 % complete ) and 3704 restraints for refining 1658 atoms. 3254 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2255 (Rfree = 0.000) for 1658 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 17: After refmac, R = 0.2188 (Rfree = 0.000) for 1648 atoms. Found 6 (12 requested) and removed 12 (6 requested) atoms. Cycle 18: After refmac, R = 0.2395 (Rfree = 0.000) for 1633 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 19: After refmac, R = 0.2059 (Rfree = 0.000) for 1631 atoms. Found 1 (12 requested) and removed 10 (6 requested) atoms. Cycle 20: After refmac, R = 0.2064 (Rfree = 0.000) for 1616 atoms. Found 3 (12 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.29 3.12 Search for helices and strands: 0 residues in 0 chains, 1665 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 1689 seeds are put forward Round 1: 127 peptides, 20 chains. Longest chain 14 peptides. Score 0.470 Round 2: 133 peptides, 20 chains. Longest chain 15 peptides. Score 0.503 Round 3: 124 peptides, 17 chains. Longest chain 17 peptides. Score 0.525 Round 4: 130 peptides, 17 chains. Longest chain 17 peptides. Score 0.555 Round 5: 128 peptides, 19 chains. Longest chain 17 peptides. Score 0.500 Taking the results from Round 4 Chains 17, Residues 113, Estimated correctness of the model 13.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3571 reflections ( 98.92 % complete ) and 3498 restraints for refining 1646 atoms. 3063 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2072 (Rfree = 0.000) for 1646 atoms. Found 7 (12 requested) and removed 12 (6 requested) atoms. Cycle 22: After refmac, R = 0.2014 (Rfree = 0.000) for 1637 atoms. Found 6 (12 requested) and removed 7 (6 requested) atoms. Cycle 23: After refmac, R = 0.1899 (Rfree = 0.000) for 1632 atoms. Found 7 (12 requested) and removed 8 (6 requested) atoms. Cycle 24: After refmac, R = 0.2014 (Rfree = 0.000) for 1625 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 25: After refmac, R = 0.2269 (Rfree = 0.000) for 1620 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.32 3.15 Search for helices and strands: 0 residues in 0 chains, 1650 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 1673 seeds are put forward Round 1: 98 peptides, 16 chains. Longest chain 16 peptides. Score 0.404 Round 2: 114 peptides, 18 chains. Longest chain 16 peptides. Score 0.446 Round 3: 115 peptides, 19 chains. Longest chain 11 peptides. Score 0.427 Round 4: 115 peptides, 17 chains. Longest chain 14 peptides. Score 0.477 Round 5: 116 peptides, 18 chains. Longest chain 14 peptides. Score 0.458 Taking the results from Round 4 Chains 18, Residues 98, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3571 reflections ( 98.92 % complete ) and 3599 restraints for refining 1656 atoms. 3184 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2459 (Rfree = 0.000) for 1656 atoms. Found 12 (12 requested) and removed 20 (6 requested) atoms. Cycle 27: After refmac, R = 0.2746 (Rfree = 0.000) for 1637 atoms. Found 6 (12 requested) and removed 30 (6 requested) atoms. Cycle 28: After refmac, R = 0.2127 (Rfree = 0.000) for 1602 atoms. Found 4 (12 requested) and removed 11 (6 requested) atoms. Cycle 29: After refmac, R = 0.1927 (Rfree = 0.000) for 1587 atoms. Found 4 (12 requested) and removed 14 (6 requested) atoms. Cycle 30: After refmac, R = 0.1784 (Rfree = 0.000) for 1573 atoms. Found 3 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.39 3.21 Search for helices and strands: 0 residues in 0 chains, 1610 seeds are put forward NCS extension: 0 residues added, 1610 seeds are put forward Round 1: 116 peptides, 21 chains. Longest chain 9 peptides. Score 0.382 Round 2: 120 peptides, 20 chains. Longest chain 11 peptides. Score 0.431 Round 3: 137 peptides, 22 chains. Longest chain 14 peptides. Score 0.478 Round 4: 140 peptides, 22 chains. Longest chain 12 peptides. Score 0.494 Round 5: 136 peptides, 20 chains. Longest chain 29 peptides. Score 0.518 Taking the results from Round 5 Chains 20, Residues 116, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3571 reflections ( 98.92 % complete ) and 3567 restraints for refining 1658 atoms. 3123 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2077 (Rfree = 0.000) for 1658 atoms. Found 7 (12 requested) and removed 8 (6 requested) atoms. Cycle 32: After refmac, R = 0.1968 (Rfree = 0.000) for 1650 atoms. Found 6 (12 requested) and removed 8 (6 requested) atoms. Cycle 33: After refmac, R = 0.1892 (Rfree = 0.000) for 1646 atoms. Found 5 (12 requested) and removed 9 (6 requested) atoms. Cycle 34: After refmac, R = 0.2625 (Rfree = 0.000) for 1641 atoms. Found 12 (12 requested) and removed 17 (6 requested) atoms. Cycle 35: After refmac, R = 0.1640 (Rfree = 0.000) for 1635 atoms. Found 4 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.38 3.20 Search for helices and strands: 0 residues in 0 chains, 1675 seeds are put forward NCS extension: 0 residues added, 1675 seeds are put forward Round 1: 73 peptides, 14 chains. Longest chain 9 peptides. Score 0.297 Round 2: 94 peptides, 15 chains. Longest chain 17 peptides. Score 0.406 Round 3: 93 peptides, 13 chains. Longest chain 23 peptides. Score 0.454 Round 4: 99 peptides, 14 chains. Longest chain 14 peptides. Score 0.462 Round 5: 90 peptides, 14 chains. Longest chain 17 peptides. Score 0.409 Taking the results from Round 4 Chains 14, Residues 85, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3571 reflections ( 98.92 % complete ) and 3724 restraints for refining 1658 atoms. 3398 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2134 (Rfree = 0.000) for 1658 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 37: After refmac, R = 0.2239 (Rfree = 0.000) for 1657 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 38: After refmac, R = 0.1661 (Rfree = 0.000) for 1658 atoms. Found 2 (12 requested) and removed 8 (6 requested) atoms. Cycle 39: After refmac, R = 0.1604 (Rfree = 0.000) for 1651 atoms. Found 1 (12 requested) and removed 6 (6 requested) atoms. Cycle 40: After refmac, R = 0.1849 (Rfree = 0.000) for 1643 atoms. Found 11 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.31 3.14 Search for helices and strands: 0 residues in 0 chains, 1678 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 1691 seeds are put forward Round 1: 77 peptides, 16 chains. Longest chain 7 peptides. Score 0.265 Round 2: 110 peptides, 18 chains. Longest chain 12 peptides. Score 0.423 Round 3: 105 peptides, 18 chains. Longest chain 12 peptides. Score 0.393 Round 4: 95 peptides, 15 chains. Longest chain 12 peptides. Score 0.412 Round 5: 118 peptides, 19 chains. Longest chain 12 peptides. Score 0.444 Taking the results from Round 5 Chains 19, Residues 99, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3571 reflections ( 98.92 % complete ) and 3643 restraints for refining 1658 atoms. 3266 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1923 (Rfree = 0.000) for 1658 atoms. Found 3 (12 requested) and removed 9 (6 requested) atoms. Cycle 42: After refmac, R = 0.1814 (Rfree = 0.000) for 1651 atoms. Found 5 (12 requested) and removed 8 (6 requested) atoms. Cycle 43: After refmac, R = 0.1712 (Rfree = 0.000) for 1648 atoms. Found 4 (12 requested) and removed 8 (6 requested) atoms. Cycle 44: After refmac, R = 0.1808 (Rfree = 0.000) for 1643 atoms. Found 8 (12 requested) and removed 11 (6 requested) atoms. Cycle 45: After refmac, R = 0.1558 (Rfree = 0.000) for 1639 atoms. Found 0 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.39 3.21 Search for helices and strands: 0 residues in 0 chains, 1674 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 1690 seeds are put forward Round 1: 85 peptides, 20 chains. Longest chain 6 peptides. Score 0.203 Round 2: 97 peptides, 16 chains. Longest chain 13 peptides. Score 0.397 Round 3: 106 peptides, 17 chains. Longest chain 16 peptides. Score 0.425 Round 4: 111 peptides, 17 chains. Longest chain 17 peptides. Score 0.454 Round 5: 105 peptides, 17 chains. Longest chain 14 peptides. Score 0.419 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 17, Residues 94, 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. 3571 reflections ( 98.92 % complete ) and 3657 restraints for refining 1658 atoms. 3298 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1912 (Rfree = 0.000) for 1658 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.1821 (Rfree = 0.000) for 1650 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.1876 (Rfree = 0.000) for 1643 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.2420 (Rfree = 0.000) for 1636 atoms. TimeTaking 30.95