Sun 23 Dec 22:22:55 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 2hsb-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hsb-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hsb-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hsb-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/2hsb-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hsb-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 22:23:04 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/2hsb-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hsb-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 99 and 0 Target number of residues in the AU: 99 Target solvent content: 0.6376 Checking the provided sequence file Detected sequence length: 126 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 126 Adjusted target solvent content: 0.54 Input MTZ file: 2hsb-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: 96 Cell parameters: 60.666 60.666 80.341 90.000 90.000 90.000 Input sequence file: 2hsb-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 1008 target number of atoms Had to go as low as 0.75 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: 48.414 3.201 Wilson plot Bfac: 70.01 2733 reflections ( 99.82 % complete ) and 0 restraints for refining 1114 atoms. Observations/parameters ratio is 0.61 ------------------------------------------------------ Starting model: R = 0.3561 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3836 (Rfree = 0.000) for 1114 atoms. Found 9 (9 requested) and removed 18 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.90 3.70 Search for helices and strands: 0 residues in 0 chains, 1141 seeds are put forward Round 1: 57 peptides, 11 chains. Longest chain 8 peptides. Score 0.329 Round 2: 64 peptides, 11 chains. Longest chain 8 peptides. Score 0.407 Round 3: 63 peptides, 10 chains. Longest chain 9 peptides. Score 0.442 Round 4: 67 peptides, 8 chains. Longest chain 14 peptides. Score 0.566 Round 5: 63 peptides, 8 chains. Longest chain 15 peptides. Score 0.530 Taking the results from Round 4 Chains 8, Residues 59, Estimated correctness of the model 31.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2733 reflections ( 99.82 % complete ) and 2017 restraints for refining 920 atoms. 1789 conditional restraints added. Observations/parameters ratio is 0.74 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3594 (Rfree = 0.000) for 920 atoms. Found 8 (8 requested) and removed 15 (4 requested) atoms. Cycle 2: After refmac, R = 0.3401 (Rfree = 0.000) for 897 atoms. Found 8 (8 requested) and removed 15 (4 requested) atoms. Cycle 3: After refmac, R = 0.3290 (Rfree = 0.000) for 879 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 4: After refmac, R = 0.3291 (Rfree = 0.000) for 875 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 5: After refmac, R = 0.3259 (Rfree = 0.000) for 871 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.63 3.44 Search for helices and strands: 0 residues in 0 chains, 912 seeds are put forward Round 1: 56 peptides, 10 chains. Longest chain 9 peptides. Score 0.366 Round 2: 80 peptides, 13 chains. Longest chain 14 peptides. Score 0.482 Round 3: 80 peptides, 14 chains. Longest chain 12 peptides. Score 0.440 Round 4: 80 peptides, 12 chains. Longest chain 12 peptides. Score 0.522 Round 5: 80 peptides, 13 chains. Longest chain 11 peptides. Score 0.482 Taking the results from Round 4 Chains 12, Residues 68, Estimated correctness of the model 18.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2733 reflections ( 99.82 % complete ) and 1873 restraints for refining 878 atoms. 1613 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3464 (Rfree = 0.000) for 878 atoms. Found 6 (7 requested) and removed 12 (3 requested) atoms. Cycle 7: After refmac, R = 0.3460 (Rfree = 0.000) for 870 atoms. Found 7 (7 requested) and removed 10 (3 requested) atoms. Cycle 8: After refmac, R = 0.3257 (Rfree = 0.000) for 859 atoms. Found 7 (7 requested) and removed 9 (3 requested) atoms. Cycle 9: After refmac, R = 0.3322 (Rfree = 0.000) for 854 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 10: After refmac, R = 0.3318 (Rfree = 0.000) for 852 atoms. Found 7 (7 requested) and removed 9 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.74 3.55 Search for helices and strands: 0 residues in 0 chains, 903 seeds are put forward Round 1: 70 peptides, 13 chains. Longest chain 9 peptides. Score 0.380 Round 2: 80 peptides, 12 chains. Longest chain 17 peptides. Score 0.522 Round 3: 62 peptides, 11 chains. Longest chain 10 peptides. Score 0.385 Round 4: 72 peptides, 11 chains. Longest chain 10 peptides. Score 0.488 Round 5: 71 peptides, 9 chains. Longest chain 11 peptides. Score 0.561 Taking the results from Round 5 Chains 9, Residues 62, Estimated correctness of the model 30.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2733 reflections ( 99.82 % complete ) and 1942 restraints for refining 888 atoms. 1703 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3490 (Rfree = 0.000) for 888 atoms. Found 7 (7 requested) and removed 14 (3 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.3684 (Rfree = 0.000) for 875 atoms. Found 7 (7 requested) and removed 13 (3 requested) atoms. Cycle 13: After refmac, R = 0.3464 (Rfree = 0.000) for 863 atoms. Found 7 (7 requested) and removed 9 (3 requested) atoms. Cycle 14: After refmac, R = 0.3560 (Rfree = 0.000) for 857 atoms. Found 7 (7 requested) and removed 9 (3 requested) atoms. Cycle 15: After refmac, R = 0.3416 (Rfree = 0.000) for 852 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.31 3.14 Search for helices and strands: 0 residues in 0 chains, 933 seeds are put forward Round 1: 49 peptides, 10 chains. Longest chain 8 peptides. Score 0.284 Round 2: 51 peptides, 8 chains. Longest chain 9 peptides. Score 0.408 Round 3: 56 peptides, 9 chains. Longest chain 10 peptides. Score 0.414 Round 4: 59 peptides, 9 chains. Longest chain 11 peptides. Score 0.446 Round 5: 53 peptides, 8 chains. Longest chain 13 peptides. Score 0.430 Taking the results from Round 4 Chains 9, Residues 50, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2733 reflections ( 99.82 % complete ) and 2155 restraints for refining 914 atoms. 1964 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3490 (Rfree = 0.000) for 914 atoms. Found 8 (8 requested) and removed 16 (4 requested) atoms. Cycle 17: After refmac, R = 0.3584 (Rfree = 0.000) for 899 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Cycle 18: After refmac, R = 0.3526 (Rfree = 0.000) for 894 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 19: After refmac, R = 0.3610 (Rfree = 0.000) for 893 atoms. Found 8 (8 requested) and removed 14 (4 requested) atoms. Cycle 20: After refmac, R = 0.3608 (Rfree = 0.000) for 881 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.24 3.07 Search for helices and strands: 0 residues in 0 chains, 933 seeds are put forward Round 1: 43 peptides, 8 chains. Longest chain 11 peptides. Score 0.315 Round 2: 51 peptides, 9 chains. Longest chain 12 peptides. Score 0.358 Round 3: 53 peptides, 9 chains. Longest chain 12 peptides. Score 0.381 Round 4: 49 peptides, 8 chains. Longest chain 12 peptides. Score 0.385 Round 5: 51 peptides, 8 chains. Longest chain 12 peptides. Score 0.408 Taking the results from Round 5 Chains 8, Residues 43, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2733 reflections ( 99.82 % complete ) and 1916 restraints for refining 869 atoms. 1752 conditional restraints added. Observations/parameters ratio is 0.79 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3640 (Rfree = 0.000) for 869 atoms. Found 7 (7 requested) and removed 10 (3 requested) atoms. Cycle 22: After refmac, R = 0.3657 (Rfree = 0.000) for 860 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 23: After refmac, R = 0.3481 (Rfree = 0.000) for 856 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 24: After refmac, R = 0.3520 (Rfree = 0.000) for 854 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 25: After refmac, R = 0.3499 (Rfree = 0.000) for 848 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.88 3.68 Search for helices and strands: 0 residues in 0 chains, 892 seeds are put forward Round 1: 41 peptides, 8 chains. Longest chain 9 peptides. Score 0.290 Round 2: 51 peptides, 9 chains. Longest chain 11 peptides. Score 0.358 Round 3: 53 peptides, 9 chains. Longest chain 13 peptides. Score 0.381 Round 4: 44 peptides, 7 chains. Longest chain 10 peptides. Score 0.379 Round 5: 48 peptides, 8 chains. Longest chain 13 peptides. Score 0.374 Taking the results from Round 3 Chains 9, Residues 44, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2733 reflections ( 99.82 % complete ) and 1688 restraints for refining 801 atoms. 1521 conditional restraints added. Observations/parameters ratio is 0.85 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3547 (Rfree = 0.000) for 801 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 27: After refmac, R = 0.3411 (Rfree = 0.000) for 797 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 28: After refmac, R = 0.3545 (Rfree = 0.000) for 794 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 29: After refmac, R = 0.3387 (Rfree = 0.000) for 788 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 30: After refmac, R = 0.3446 (Rfree = 0.000) for 788 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.16 3.00 Search for helices and strands: 0 residues in 0 chains, 831 seeds are put forward Round 1: 51 peptides, 11 chains. Longest chain 7 peptides. Score 0.257 Round 2: 59 peptides, 10 chains. Longest chain 12 peptides. Score 0.399 Round 3: 61 peptides, 10 chains. Longest chain 14 peptides. Score 0.421 Round 4: 66 peptides, 12 chains. Longest chain 10 peptides. Score 0.382 Round 5: 64 peptides, 10 chains. Longest chain 15 peptides. Score 0.452 Taking the results from Round 5 Chains 10, Residues 54, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2733 reflections ( 99.82 % complete ) and 1751 restraints for refining 839 atoms. 1545 conditional restraints added. Observations/parameters ratio is 0.81 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3509 (Rfree = 0.000) for 839 atoms. Found 7 (7 requested) and removed 11 (3 requested) atoms. Cycle 32: After refmac, R = 0.3595 (Rfree = 0.000) for 829 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 33: After refmac, R = 0.3413 (Rfree = 0.000) for 824 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 34: After refmac, R = 0.3438 (Rfree = 0.000) for 821 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 35: After refmac, R = 0.3478 (Rfree = 0.000) for 819 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.61 3.42 Search for helices and strands: 0 residues in 0 chains, 869 seeds are put forward Round 1: 50 peptides, 9 chains. Longest chain 13 peptides. Score 0.347 Round 2: 59 peptides, 9 chains. Longest chain 17 peptides. Score 0.446 Round 3: 61 peptides, 9 chains. Longest chain 17 peptides. Score 0.466 Round 4: 64 peptides, 9 chains. Longest chain 17 peptides. Score 0.496 Round 5: 60 peptides, 8 chains. Longest chain 14 peptides. Score 0.501 Taking the results from Round 5 Chains 8, Residues 52, Estimated correctness of the model 11.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2733 reflections ( 99.82 % complete ) and 1801 restraints for refining 838 atoms. 1601 conditional restraints added. Observations/parameters ratio is 0.82 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3516 (Rfree = 0.000) for 838 atoms. Found 7 (7 requested) and removed 11 (3 requested) atoms. Cycle 37: After refmac, R = 0.3330 (Rfree = 0.000) for 827 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 38: After refmac, R = 0.3416 (Rfree = 0.000) for 823 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 39: After refmac, R = 0.3452 (Rfree = 0.000) for 823 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 40: After refmac, R = 0.3503 (Rfree = 0.000) for 824 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.26 3.09 Search for helices and strands: 0 residues in 0 chains, 867 seeds are put forward Round 1: 49 peptides, 9 chains. Longest chain 11 peptides. Score 0.335 Round 2: 63 peptides, 9 chains. Longest chain 13 peptides. Score 0.486 Round 3: 61 peptides, 9 chains. Longest chain 13 peptides. Score 0.466 Round 4: 61 peptides, 9 chains. Longest chain 13 peptides. Score 0.466 Round 5: 64 peptides, 8 chains. Longest chain 13 peptides. Score 0.539 Taking the results from Round 5 Chains 8, Residues 56, Estimated correctness of the model 23.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2733 reflections ( 99.82 % complete ) and 1779 restraints for refining 847 atoms. 1563 conditional restraints added. Observations/parameters ratio is 0.81 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3454 (Rfree = 0.000) for 847 atoms. Found 7 (7 requested) and removed 12 (3 requested) atoms. Cycle 42: After refmac, R = 0.3474 (Rfree = 0.000) for 839 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 43: After refmac, R = 0.3446 (Rfree = 0.000) for 837 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 44: After refmac, R = 0.3375 (Rfree = 0.000) for 833 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 45: After refmac, R = 0.3537 (Rfree = 0.000) for 832 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.24 3.07 Search for helices and strands: 0 residues in 0 chains, 862 seeds are put forward Round 1: 47 peptides, 9 chains. Longest chain 10 peptides. Score 0.311 Round 2: 53 peptides, 9 chains. Longest chain 11 peptides. Score 0.381 Round 3: 46 peptides, 7 chains. Longest chain 11 peptides. Score 0.402 Round 4: 55 peptides, 9 chains. Longest chain 11 peptides. Score 0.403 Round 5: 50 peptides, 8 chains. Longest chain 11 peptides. Score 0.397 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 9, Residues 46, 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 2hsb-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2733 reflections ( 99.82 % complete ) and 1756 restraints for refining 850 atoms. 1581 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3440 (Rfree = 0.000) for 850 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.3239 (Rfree = 0.000) for 842 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.3210 (Rfree = 0.000) for 839 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.3224 (Rfree = 0.000) for 835 atoms. TimeTaking 22.52