Sun 23 Dec 22:22:41 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 2hcf-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hcf-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hcf-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hcf-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/2hcf-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hcf-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 22:22:50 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/2hcf-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hcf-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 156 and 0 Target number of residues in the AU: 156 Target solvent content: 0.6245 Checking the provided sequence file Detected sequence length: 234 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 234 Adjusted target solvent content: 0.44 Input MTZ file: 2hcf-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: 19 Cell parameters: 37.750 71.590 83.200 90.000 90.000 90.000 Input sequence file: 2hcf-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 1872 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: 54.266 3.200 Wilson plot Bfac: 62.56 4009 reflections ( 99.45 % complete ) and 0 restraints for refining 2076 atoms. Observations/parameters ratio is 0.48 ------------------------------------------------------ Starting model: R = 0.3300 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2682 (Rfree = 0.000) for 2076 atoms. Found 13 (18 requested) and removed 34 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.19 3.46 Search for helices and strands: 0 residues in 0 chains, 2119 seeds are put forward Round 1: 107 peptides, 22 chains. Longest chain 9 peptides. Score 0.316 Round 2: 123 peptides, 20 chains. Longest chain 12 peptides. Score 0.485 Round 3: 130 peptides, 15 chains. Longest chain 20 peptides. Score 0.646 Round 4: 128 peptides, 15 chains. Longest chain 21 peptides. Score 0.637 Round 5: 131 peptides, 15 chains. Longest chain 16 peptides. Score 0.651 Taking the results from Round 5 Chains 15, Residues 116, Estimated correctness of the model 54.1 % 2 chains (27 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 4009 reflections ( 99.45 % complete ) and 3547 restraints for refining 1708 atoms. 2995 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2570 (Rfree = 0.000) for 1708 atoms. Found 13 (15 requested) and removed 20 (7 requested) atoms. Cycle 2: After refmac, R = 0.2368 (Rfree = 0.000) for 1681 atoms. Found 6 (15 requested) and removed 9 (7 requested) atoms. Cycle 3: After refmac, R = 0.2419 (Rfree = 0.000) for 1676 atoms. Found 10 (15 requested) and removed 13 (7 requested) atoms. Cycle 4: After refmac, R = 0.2182 (Rfree = 0.000) for 1666 atoms. Found 2 (15 requested) and removed 8 (7 requested) atoms. Cycle 5: After refmac, R = 0.2174 (Rfree = 0.000) for 1657 atoms. Found 3 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.12 3.38 Search for helices and strands: 0 residues in 0 chains, 1723 seeds are put forward Round 1: 115 peptides, 20 chains. Longest chain 12 peptides. Score 0.433 Round 2: 125 peptides, 19 chains. Longest chain 13 peptides. Score 0.524 Round 3: 128 peptides, 19 chains. Longest chain 17 peptides. Score 0.541 Round 4: 138 peptides, 17 chains. Longest chain 17 peptides. Score 0.641 Round 5: 137 peptides, 19 chains. Longest chain 17 peptides. Score 0.591 Taking the results from Round 4 Chains 20, Residues 121, Estimated correctness of the model 51.6 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 4009 reflections ( 99.45 % complete ) and 3599 restraints for refining 1709 atoms. 3061 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2442 (Rfree = 0.000) for 1709 atoms. Found 8 (15 requested) and removed 14 (7 requested) atoms. Cycle 7: After refmac, R = 0.2267 (Rfree = 0.000) for 1698 atoms. Found 6 (15 requested) and removed 12 (7 requested) atoms. Cycle 8: After refmac, R = 0.2205 (Rfree = 0.000) for 1689 atoms. Found 8 (15 requested) and removed 11 (7 requested) atoms. Cycle 9: After refmac, R = 0.2107 (Rfree = 0.000) for 1681 atoms. Found 3 (15 requested) and removed 7 (7 requested) atoms. Cycle 10: After refmac, R = 0.2006 (Rfree = 0.000) for 1674 atoms. Found 0 (15 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.17 3.44 Search for helices and strands: 0 residues in 0 chains, 1733 seeds are put forward Round 1: 126 peptides, 22 chains. Longest chain 13 peptides. Score 0.449 Round 2: 129 peptides, 18 chains. Longest chain 16 peptides. Score 0.572 Round 3: 141 peptides, 22 chains. Longest chain 14 peptides. Score 0.541 Round 4: 145 peptides, 21 chains. Longest chain 15 peptides. Score 0.587 Round 5: 150 peptides, 22 chains. Longest chain 15 peptides. Score 0.590 Taking the results from Round 5 Chains 22, Residues 128, Estimated correctness of the model 38.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4009 reflections ( 99.45 % complete ) and 3847 restraints for refining 1709 atoms. 3357 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2251 (Rfree = 0.000) for 1709 atoms. Found 15 (15 requested) and removed 10 (7 requested) atoms. Cycle 12: After refmac, R = 0.2166 (Rfree = 0.000) for 1711 atoms. Found 7 (15 requested) and removed 10 (7 requested) atoms. Cycle 13: After refmac, R = 0.2387 (Rfree = 0.000) for 1706 atoms. Found 6 (15 requested) and removed 10 (7 requested) atoms. Cycle 14: After refmac, R = 0.1897 (Rfree = 0.000) for 1697 atoms. Found 4 (15 requested) and removed 11 (7 requested) atoms. Cycle 15: After refmac, R = 0.1787 (Rfree = 0.000) for 1687 atoms. Found 3 (15 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.17 3.44 Search for helices and strands: 0 residues in 0 chains, 1761 seeds are put forward Round 1: 118 peptides, 21 chains. Longest chain 12 peptides. Score 0.424 Round 2: 129 peptides, 18 chains. Longest chain 19 peptides. Score 0.572 Round 3: 135 peptides, 17 chains. Longest chain 21 peptides. Score 0.626 Round 4: 126 peptides, 17 chains. Longest chain 29 peptides. Score 0.580 Round 5: 128 peptides, 17 chains. Longest chain 17 peptides. Score 0.590 Taking the results from Round 3 Chains 17, Residues 118, Estimated correctness of the model 47.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4009 reflections ( 99.45 % complete ) and 3792 restraints for refining 1709 atoms. 3337 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2018 (Rfree = 0.000) for 1709 atoms. Found 12 (15 requested) and removed 10 (7 requested) atoms. Cycle 17: After refmac, R = 0.1892 (Rfree = 0.000) for 1704 atoms. Found 3 (15 requested) and removed 7 (7 requested) atoms. Cycle 18: After refmac, R = 0.1887 (Rfree = 0.000) for 1698 atoms. Found 3 (15 requested) and removed 7 (7 requested) atoms. Cycle 19: After refmac, R = 0.1840 (Rfree = 0.000) for 1691 atoms. Found 9 (15 requested) and removed 7 (7 requested) atoms. Cycle 20: After refmac, R = 0.1816 (Rfree = 0.000) for 1689 atoms. Found 3 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.14 3.40 Search for helices and strands: 0 residues in 0 chains, 1743 seeds are put forward Round 1: 104 peptides, 20 chains. Longest chain 8 peptides. Score 0.356 Round 2: 125 peptides, 20 chains. Longest chain 15 peptides. Score 0.497 Round 3: 122 peptides, 19 chains. Longest chain 20 peptides. Score 0.505 Round 4: 130 peptides, 16 chains. Longest chain 26 peptides. Score 0.624 Round 5: 127 peptides, 17 chains. Longest chain 26 peptides. Score 0.585 Taking the results from Round 4 Chains 16, Residues 114, Estimated correctness of the model 47.4 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 4009 reflections ( 99.45 % complete ) and 3696 restraints for refining 1709 atoms. 3198 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2129 (Rfree = 0.000) for 1709 atoms. Found 10 (15 requested) and removed 12 (7 requested) atoms. Cycle 22: After refmac, R = 0.2057 (Rfree = 0.000) for 1699 atoms. Found 11 (15 requested) and removed 13 (7 requested) atoms. Cycle 23: After refmac, R = 0.1865 (Rfree = 0.000) for 1691 atoms. Found 6 (15 requested) and removed 8 (7 requested) atoms. Cycle 24: After refmac, R = 0.1660 (Rfree = 0.000) for 1686 atoms. Found 3 (15 requested) and removed 8 (7 requested) atoms. Cycle 25: After refmac, R = 0.1569 (Rfree = 0.000) for 1680 atoms. Found 1 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.14 3.40 Search for helices and strands: 0 residues in 0 chains, 1730 seeds are put forward Round 1: 90 peptides, 18 chains. Longest chain 10 peptides. Score 0.314 Round 2: 113 peptides, 19 chains. Longest chain 12 peptides. Score 0.448 Round 3: 115 peptides, 20 chains. Longest chain 12 peptides. Score 0.433 Round 4: 122 peptides, 21 chains. Longest chain 15 peptides. Score 0.451 Round 5: 122 peptides, 19 chains. Longest chain 16 peptides. Score 0.505 Taking the results from Round 5 Chains 19, Residues 103, Estimated correctness of the model 12.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4009 reflections ( 99.45 % complete ) and 3954 restraints for refining 1709 atoms. 3561 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1938 (Rfree = 0.000) for 1709 atoms. Found 13 (15 requested) and removed 8 (7 requested) atoms. Cycle 27: After refmac, R = 0.1759 (Rfree = 0.000) for 1713 atoms. Found 4 (15 requested) and removed 7 (7 requested) atoms. Cycle 28: After refmac, R = 0.1750 (Rfree = 0.000) for 1708 atoms. Found 6 (15 requested) and removed 7 (7 requested) atoms. Cycle 29: After refmac, R = 0.1711 (Rfree = 0.000) for 1703 atoms. Found 5 (15 requested) and removed 7 (7 requested) atoms. Cycle 30: After refmac, R = 0.1659 (Rfree = 0.000) for 1699 atoms. Found 5 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.17 3.44 Search for helices and strands: 0 residues in 0 chains, 1759 seeds are put forward Round 1: 73 peptides, 13 chains. Longest chain 13 peptides. Score 0.347 Round 2: 90 peptides, 14 chains. Longest chain 15 peptides. Score 0.439 Round 3: 95 peptides, 17 chains. Longest chain 13 peptides. Score 0.383 Round 4: 99 peptides, 16 chains. Longest chain 15 peptides. Score 0.441 Round 5: 95 peptides, 16 chains. Longest chain 15 peptides. Score 0.413 Taking the results from Round 4 Chains 16, Residues 83, Estimated correctness of the model 0.0 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 4009 reflections ( 99.45 % complete ) and 3842 restraints for refining 1709 atoms. 3480 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1815 (Rfree = 0.000) for 1709 atoms. Found 12 (15 requested) and removed 8 (7 requested) atoms. Cycle 32: After refmac, R = 0.1675 (Rfree = 0.000) for 1712 atoms. Found 3 (15 requested) and removed 7 (7 requested) atoms. Cycle 33: After refmac, R = 0.1604 (Rfree = 0.000) for 1707 atoms. Found 4 (15 requested) and removed 7 (7 requested) atoms. Cycle 34: After refmac, R = 0.1890 (Rfree = 0.000) for 1703 atoms. Found 15 (15 requested) and removed 7 (7 requested) atoms. Cycle 35: After refmac, R = 0.1657 (Rfree = 0.000) for 1710 atoms. Found 13 (15 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.12 3.38 Search for helices and strands: 0 residues in 0 chains, 1777 seeds are put forward Round 1: 78 peptides, 14 chains. Longest chain 11 peptides. Score 0.352 Round 2: 99 peptides, 17 chains. Longest chain 13 peptides. Score 0.411 Round 3: 99 peptides, 16 chains. Longest chain 13 peptides. Score 0.441 Round 4: 99 peptides, 14 chains. Longest chain 23 peptides. Score 0.499 Round 5: 96 peptides, 15 chains. Longest chain 13 peptides. Score 0.450 Taking the results from Round 4 Chains 15, Residues 85, Estimated correctness of the model 11.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4009 reflections ( 99.45 % complete ) and 3806 restraints for refining 1709 atoms. 3450 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1814 (Rfree = 0.000) for 1709 atoms. Found 7 (15 requested) and removed 8 (7 requested) atoms. Cycle 37: After refmac, R = 0.1711 (Rfree = 0.000) for 1706 atoms. Found 5 (15 requested) and removed 7 (7 requested) atoms. Cycle 38: After refmac, R = 0.1698 (Rfree = 0.000) for 1702 atoms. Found 12 (15 requested) and removed 7 (7 requested) atoms. Cycle 39: After refmac, R = 0.1502 (Rfree = 0.000) for 1705 atoms. Found 8 (15 requested) and removed 7 (7 requested) atoms. Cycle 40: After refmac, R = 0.1580 (Rfree = 0.000) for 1706 atoms. Found 6 (15 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.16 3.42 Search for helices and strands: 0 residues in 0 chains, 1746 seeds are put forward Round 1: 80 peptides, 17 chains. Longest chain 8 peptides. Score 0.268 Round 2: 93 peptides, 15 chains. Longest chain 13 peptides. Score 0.430 Round 3: 104 peptides, 18 chains. Longest chain 15 peptides. Score 0.416 Round 4: 102 peptides, 18 chains. Longest chain 13 peptides. Score 0.402 Round 5: 100 peptides, 17 chains. Longest chain 14 peptides. Score 0.418 Taking the results from Round 2 Chains 16, Residues 78, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4009 reflections ( 99.45 % complete ) and 3823 restraints for refining 1709 atoms. 3499 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1801 (Rfree = 0.000) for 1709 atoms. Found 13 (15 requested) and removed 7 (7 requested) atoms. Cycle 42: After refmac, R = 0.1664 (Rfree = 0.000) for 1709 atoms. Found 11 (15 requested) and removed 7 (7 requested) atoms. Cycle 43: After refmac, R = 0.1702 (Rfree = 0.000) for 1711 atoms. Found 9 (15 requested) and removed 7 (7 requested) atoms. Cycle 44: After refmac, R = 0.1654 (Rfree = 0.000) for 1711 atoms. Found 10 (15 requested) and removed 7 (7 requested) atoms. Cycle 45: After refmac, R = 0.2066 (Rfree = 0.000) for 1712 atoms. Found 15 (15 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.13 3.39 Search for helices and strands: 0 residues in 0 chains, 1782 seeds are put forward Round 1: 65 peptides, 14 chains. Longest chain 7 peptides. Score 0.247 Round 2: 86 peptides, 16 chains. Longest chain 11 peptides. Score 0.348 Round 3: 95 peptides, 16 chains. Longest chain 11 peptides. Score 0.413 Round 4: 91 peptides, 15 chains. Longest chain 10 peptides. Score 0.416 Round 5: 96 peptides, 16 chains. Longest chain 10 peptides. Score 0.420 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 16, Residues 80, 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 2hcf-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4009 reflections ( 99.45 % complete ) and 3893 restraints for refining 1709 atoms. 3589 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1850 (Rfree = 0.000) for 1709 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.1687 (Rfree = 0.000) for 1696 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.1552 (Rfree = 0.000) for 1686 atoms. Found 0 (15 requested) and removed 4 (7 requested) atoms. Cycle 49: After refmac, R = 0.1551 (Rfree = 0.000) for 1681 atoms. TimeTaking 30.53