Sun 23 Dec 22:22:42 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 2etd-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2etd-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2etd-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2etd-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/2etd-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2etd-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 22:22:52 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/2etd-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2etd-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 124 and 0 Target number of residues in the AU: 124 Target solvent content: 0.6332 Checking the provided sequence file Detected sequence length: 171 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 171 Adjusted target solvent content: 0.49 Input MTZ file: 2etd-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: 21 Cell parameters: 80.417 85.225 53.388 90.000 90.000 90.000 Input sequence file: 2etd-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 1368 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: 58.489 3.401 Wilson plot Bfac: 68.11 2262 reflections ( 83.35 % complete ) and 0 restraints for refining 1524 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Starting model: R = 0.3812 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.4114 (Rfree = 0.000) for 1524 atoms. Found 3 (11 requested) and removed 31 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.51 3.56 Search for helices and strands: 0 residues in 0 chains, 1529 seeds are put forward Round 1: 34 peptides, 8 chains. Longest chain 6 peptides. Score 0.192 Round 2: 37 peptides, 7 chains. Longest chain 9 peptides. Score 0.278 Round 3: 42 peptides, 9 chains. Longest chain 7 peptides. Score 0.237 Round 4: 55 peptides, 9 chains. Longest chain 13 peptides. Score 0.371 Round 5: 56 peptides, 10 chains. Longest chain 9 peptides. Score 0.338 Taking the results from Round 4 Chains 9, Residues 46, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2262 reflections ( 83.35 % complete ) and 2874 restraints for refining 1183 atoms. 2699 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3836 (Rfree = 0.000) for 1183 atoms. Found 4 (8 requested) and removed 14 (4 requested) atoms. Cycle 2: After refmac, R = 0.3714 (Rfree = 0.000) for 1149 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 3: After refmac, R = 0.3824 (Rfree = 0.000) for 1130 atoms. Found 3 (8 requested) and removed 19 (4 requested) atoms. Cycle 4: After refmac, R = 0.3607 (Rfree = 0.000) for 1100 atoms. Found 2 (8 requested) and removed 10 (4 requested) atoms. Cycle 5: After refmac, R = 0.3537 (Rfree = 0.000) for 1087 atoms. Found 0 (8 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.24 3.28 Search for helices and strands: 0 residues in 0 chains, 1123 seeds are put forward Round 1: 40 peptides, 9 chains. Longest chain 6 peptides. Score 0.215 Round 2: 61 peptides, 11 chains. Longest chain 9 peptides. Score 0.345 Round 3: 63 peptides, 11 chains. Longest chain 8 peptides. Score 0.364 Round 4: 66 peptides, 11 chains. Longest chain 9 peptides. Score 0.391 Round 5: 68 peptides, 11 chains. Longest chain 9 peptides. Score 0.409 Taking the results from Round 5 Chains 11, Residues 57, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2262 reflections ( 83.35 % complete ) and 2016 restraints for refining 967 atoms. 1799 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3771 (Rfree = 0.000) for 967 atoms. Found 7 (7 requested) and removed 45 (3 requested) atoms. Cycle 7: After refmac, R = 0.3330 (Rfree = 0.000) for 913 atoms. Found 7 (7 requested) and removed 18 (3 requested) atoms. Cycle 8: After refmac, R = 0.3369 (Rfree = 0.000) for 896 atoms. Found 6 (6 requested) and removed 20 (3 requested) atoms. Cycle 9: After refmac, R = 0.3201 (Rfree = 0.000) for 873 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 10: After refmac, R = 0.3086 (Rfree = 0.000) for 864 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.41 3.46 Search for helices and strands: 0 residues in 0 chains, 923 seeds are put forward Round 1: 57 peptides, 12 chains. Longest chain 7 peptides. Score 0.263 Round 2: 59 peptides, 10 chains. Longest chain 9 peptides. Score 0.367 Round 3: 65 peptides, 10 chains. Longest chain 11 peptides. Score 0.421 Round 4: 72 peptides, 10 chains. Longest chain 14 peptides. Score 0.480 Round 5: 66 peptides, 9 chains. Longest chain 12 peptides. Score 0.468 Taking the results from Round 4 Chains 10, Residues 62, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2262 reflections ( 83.35 % complete ) and 1871 restraints for refining 908 atoms. 1633 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3555 (Rfree = 0.000) for 908 atoms. Found 6 (6 requested) and removed 12 (3 requested) atoms. Cycle 12: After refmac, R = 0.3365 (Rfree = 0.000) for 891 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. Cycle 13: After refmac, R = 0.3258 (Rfree = 0.000) for 886 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. Cycle 14: After refmac, R = 0.3197 (Rfree = 0.000) for 879 atoms. Found 6 (6 requested) and removed 15 (3 requested) atoms. Cycle 15: After refmac, R = 0.3321 (Rfree = 0.000) for 865 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.45 3.50 Search for helices and strands: 0 residues in 0 chains, 939 seeds are put forward Round 1: 51 peptides, 10 chains. Longest chain 7 peptides. Score 0.288 Round 2: 60 peptides, 11 chains. Longest chain 8 peptides. Score 0.335 Round 3: 59 peptides, 9 chains. Longest chain 10 peptides. Score 0.408 Round 4: 59 peptides, 10 chains. Longest chain 8 peptides. Score 0.367 Round 5: 67 peptides, 11 chains. Longest chain 10 peptides. Score 0.400 Taking the results from Round 3 Chains 9, Residues 50, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2262 reflections ( 83.35 % complete ) and 1797 restraints for refining 877 atoms. 1606 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3754 (Rfree = 0.000) for 877 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 17: After refmac, R = 0.3509 (Rfree = 0.000) for 870 atoms. Found 6 (6 requested) and removed 12 (3 requested) atoms. Cycle 18: After refmac, R = 0.3352 (Rfree = 0.000) for 856 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 19: After refmac, R = 0.3359 (Rfree = 0.000) for 847 atoms. Found 4 (6 requested) and removed 19 (3 requested) atoms. Cycle 20: After refmac, R = 0.3514 (Rfree = 0.000) for 825 atoms. Found 6 (6 requested) and removed 94 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.36 3.41 Search for helices and strands: 0 residues in 0 chains, 773 seeds are put forward Round 1: 45 peptides, 10 chains. Longest chain 7 peptides. Score 0.224 Round 2: 51 peptides, 10 chains. Longest chain 6 peptides. Score 0.288 Round 3: 49 peptides, 10 chains. Longest chain 8 peptides. Score 0.268 Round 4: 49 peptides, 10 chains. Longest chain 7 peptides. Score 0.268 Round 5: 48 peptides, 10 chains. Longest chain 8 peptides. Score 0.257 Taking the results from Round 2 Chains 10, Residues 41, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2262 reflections ( 83.35 % complete ) and 1695 restraints for refining 798 atoms. 1541 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 21: After refmac, R = 0.4308 (Rfree = 0.000) for 798 atoms. Found 6 (6 requested) and removed 37 (3 requested) atoms. Cycle 22: After refmac, R = 0.3882 (Rfree = 0.000) for 758 atoms. Found 3 (5 requested) and removed 10 (2 requested) atoms. Cycle 23: After refmac, R = 0.3587 (Rfree = 0.000) for 742 atoms. Found 5 (5 requested) and removed 12 (2 requested) atoms. Cycle 24: After refmac, R = 0.4059 (Rfree = 0.000) for 731 atoms. Found 5 (5 requested) and removed 12 (2 requested) atoms. Cycle 25: After refmac, R = 0.4199 (Rfree = 0.000) for 717 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 4.06 4.11 Search for helices and strands: 0 residues in 0 chains, 746 seeds are put forward Round 1: 21 peptides, 4 chains. Longest chain 7 peptides. Score 0.246 Round 2: 33 peptides, 5 chains. Longest chain 11 peptides. Score 0.334 Round 3: 33 peptides, 5 chains. Longest chain 14 peptides. Score 0.334 Round 4: 35 peptides, 5 chains. Longest chain 13 peptides. Score 0.355 Round 5: 39 peptides, 7 chains. Longest chain 10 peptides. Score 0.299 Taking the results from Round 4 Chains 5, Residues 30, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2262 reflections ( 83.35 % complete ) and 1600 restraints for refining 709 atoms. 1485 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 26: After refmac, R = 0.4576 (Rfree = 0.000) for 709 atoms. Found 3 (5 requested) and removed 17 (2 requested) atoms. Cycle 27: After refmac, R = 0.4414 (Rfree = 0.000) for 688 atoms. Found 3 (5 requested) and removed 23 (2 requested) atoms. Cycle 28: After refmac, R = 0.4043 (Rfree = 0.000) for 662 atoms. Found 4 (5 requested) and removed 17 (2 requested) atoms. Cycle 29: After refmac, R = 0.4158 (Rfree = 0.000) for 642 atoms. Found 4 (4 requested) and removed 18 (2 requested) atoms. Cycle 30: After refmac, R = 0.4160 (Rfree = 0.000) for 624 atoms. Found 1 (4 requested) and removed 17 (2 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.92 3.97 Search for helices and strands: 0 residues in 0 chains, 640 seeds are put forward Round 1: 33 peptides, 8 chains. Longest chain 5 peptides. Score 0.180 Round 2: 53 peptides, 11 chains. Longest chain 7 peptides. Score 0.265 Round 3: 57 peptides, 11 chains. Longest chain 8 peptides. Score 0.306 Round 4: 61 peptides, 12 chains. Longest chain 8 peptides. Score 0.303 Round 5: 63 peptides, 13 chains. Longest chain 7 peptides. Score 0.282 Taking the results from Round 3 Chains 11, Residues 46, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2262 reflections ( 83.35 % complete ) and 1384 restraints for refining 697 atoms. 1211 conditional restraints added. Observations/parameters ratio is 0.81 ------------------------------------------------------ Cycle 31: After refmac, R = 0.4199 (Rfree = 0.000) for 697 atoms. Found 2 (5 requested) and removed 6 (2 requested) atoms. Cycle 32: After refmac, R = 0.3946 (Rfree = 0.000) for 686 atoms. Found 3 (5 requested) and removed 7 (2 requested) atoms. Cycle 33: After refmac, R = 0.3774 (Rfree = 0.000) for 677 atoms. Found 2 (5 requested) and removed 6 (2 requested) atoms. Cycle 34: After refmac, R = 0.4087 (Rfree = 0.000) for 670 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 35: After refmac, R = 0.3891 (Rfree = 0.000) for 669 atoms. Found 1 (5 requested) and removed 7 (2 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.80 3.85 Search for helices and strands: 0 residues in 0 chains, 705 seeds are put forward Round 1: 52 peptides, 12 chains. Longest chain 7 peptides. Score 0.211 Round 2: 62 peptides, 12 chains. Longest chain 12 peptides. Score 0.313 Round 3: 55 peptides, 10 chains. Longest chain 9 peptides. Score 0.329 Round 4: 60 peptides, 12 chains. Longest chain 7 peptides. Score 0.293 Round 5: 60 peptides, 12 chains. Longest chain 9 peptides. Score 0.293 Taking the results from Round 3 Chains 10, Residues 45, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2262 reflections ( 83.35 % complete ) and 1538 restraints for refining 736 atoms. 1368 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 36: After refmac, R = 0.4160 (Rfree = 0.000) for 736 atoms. Found 4 (5 requested) and removed 10 (2 requested) atoms. Cycle 37: After refmac, R = 0.3980 (Rfree = 0.000) for 726 atoms. Found 3 (5 requested) and removed 8 (2 requested) atoms. Cycle 38: After refmac, R = 0.3829 (Rfree = 0.000) for 718 atoms. Found 1 (5 requested) and removed 11 (2 requested) atoms. Cycle 39: After refmac, R = 0.3700 (Rfree = 0.000) for 707 atoms. Found 2 (5 requested) and removed 3 (2 requested) atoms. Cycle 40: After refmac, R = 0.3587 (Rfree = 0.000) for 705 atoms. Found 1 (5 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.94 3.99 Search for helices and strands: 0 residues in 0 chains, 747 seeds are put forward Round 1: 49 peptides, 9 chains. Longest chain 9 peptides. Score 0.312 Round 2: 63 peptides, 11 chains. Longest chain 8 peptides. Score 0.364 Round 3: 60 peptides, 12 chains. Longest chain 8 peptides. Score 0.293 Round 4: 56 peptides, 11 chains. Longest chain 8 peptides. Score 0.296 Round 5: 62 peptides, 12 chains. Longest chain 8 peptides. Score 0.313 Taking the results from Round 2 Chains 11, Residues 52, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 2262 reflections ( 83.35 % complete ) and 1510 restraints for refining 785 atoms. 1292 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3868 (Rfree = 0.000) for 785 atoms. Found 5 (5 requested) and removed 6 (2 requested) atoms. Cycle 42: After refmac, R = 0.3830 (Rfree = 0.000) for 778 atoms. Found 4 (5 requested) and removed 5 (2 requested) atoms. Cycle 43: After refmac, R = 0.3693 (Rfree = 0.000) for 774 atoms. Found 1 (5 requested) and removed 4 (2 requested) atoms. Cycle 44: After refmac, R = 0.3258 (Rfree = 0.000) for 765 atoms. Found 3 (5 requested) and removed 3 (2 requested) atoms. Cycle 45: After refmac, R = 0.3636 (Rfree = 0.000) for 764 atoms. Found 4 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 4.04 4.09 Search for helices and strands: 0 residues in 0 chains, 783 seeds are put forward Round 1: 40 peptides, 10 chains. Longest chain 4 peptides. Score 0.167 Round 2: 46 peptides, 10 chains. Longest chain 7 peptides. Score 0.235 Round 3: 48 peptides, 10 chains. Longest chain 6 peptides. Score 0.257 Round 4: 47 peptides, 10 chains. Longest chain 7 peptides. Score 0.246 Round 5: 50 peptides, 10 chains. Longest chain 8 peptides. Score 0.278 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 10, Residues 40, 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 2etd-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2262 reflections ( 83.35 % complete ) and 1878 restraints for refining 834 atoms. 1728 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3900 (Rfree = 0.000) for 834 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.3718 (Rfree = 0.000) for 826 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.3804 (Rfree = 0.000) for 819 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.3841 (Rfree = 0.000) for 811 atoms. TimeTaking 23.5