Sun 23 Dec 23:48:58 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vpz-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vpz-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vpz-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vpz-3.4-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/1vpz-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vpz-3.4-parrot-mrncs ############### 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 23:49:02 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/mrncs/ArpWArp/wArpResults/WorkingDir/1vpz-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vpz-3.4-parrot-mrncs/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 88 and 0 Target number of residues in the AU: 88 Target solvent content: 0.6520 Checking the provided sequence file Detected sequence length: 73 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 146 Adjusted target solvent content: 0.42 Input MTZ file: 1vpz-3.4-parrot-mrncs.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: 20 Cell parameters: 49.075 56.647 98.468 90.000 90.000 90.000 Input sequence file: 1vpz-3.4-parrot-mrncs.fasta_lf Building free atoms model in initial map for 1168 target number of atoms Had to go as low as 0.50 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: 24.580 3.400 Wilson plot Bfac: 78.62 2008 reflections ( 98.14 % complete ) and 0 restraints for refining 1300 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Starting model: R = 0.3453 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3122 (Rfree = 0.000) for 1300 atoms. Found 5 (9 requested) and removed 96 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.58 3.99 Search for helices and strands: 0 residues in 0 chains, 1215 seeds are put forward NCS extension: 0 residues added, 1215 seeds are put forward Round 1: 29 peptides, 7 chains. Longest chain 5 peptides. Score 0.183 Round 2: 47 peptides, 11 chains. Longest chain 5 peptides. Score 0.209 Round 3: 51 peptides, 12 chains. Longest chain 5 peptides. Score 0.208 Round 4: 57 peptides, 13 chains. Longest chain 6 peptides. Score 0.234 Round 5: 63 peptides, 14 chains. Longest chain 6 peptides. Score 0.258 Taking the results from Round 5 Chains 14, Residues 49, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2008 reflections ( 98.14 % complete ) and 2387 restraints for refining 1002 atoms. 2205 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3621 (Rfree = 0.000) for 1002 atoms. Found 7 (7 requested) and removed 23 (3 requested) atoms. Cycle 2: After refmac, R = 0.3425 (Rfree = 0.000) for 983 atoms. Found 7 (7 requested) and removed 17 (3 requested) atoms. Cycle 3: After refmac, R = 0.3319 (Rfree = 0.000) for 970 atoms. Found 4 (7 requested) and removed 28 (3 requested) atoms. Cycle 4: After refmac, R = 0.3219 (Rfree = 0.000) for 945 atoms. Found 1 (7 requested) and removed 9 (3 requested) atoms. Cycle 5: After refmac, R = 0.3171 (Rfree = 0.000) for 930 atoms. Found 4 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.87 3.20 Search for helices and strands: 0 residues in 0 chains, 960 seeds are put forward NCS extension: 0 residues added, 960 seeds are put forward Round 1: 41 peptides, 9 chains. Longest chain 7 peptides. Score 0.239 Round 2: 49 peptides, 9 chains. Longest chain 12 peptides. Score 0.345 Round 3: 49 peptides, 9 chains. Longest chain 10 peptides. Score 0.345 Round 4: 52 peptides, 9 chains. Longest chain 9 peptides. Score 0.382 Round 5: 49 peptides, 11 chains. Longest chain 7 peptides. Score 0.236 Taking the results from Round 4 Chains 9, Residues 43, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2008 reflections ( 98.14 % complete ) and 2248 restraints for refining 928 atoms. 2085 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3112 (Rfree = 0.000) for 928 atoms. Found 2 (7 requested) and removed 17 (3 requested) atoms. Cycle 7: After refmac, R = 0.2974 (Rfree = 0.000) for 904 atoms. Found 5 (6 requested) and removed 12 (3 requested) atoms. Cycle 8: After refmac, R = 0.2945 (Rfree = 0.000) for 891 atoms. Found 2 (6 requested) and removed 20 (3 requested) atoms. Cycle 9: After refmac, R = 0.2979 (Rfree = 0.000) for 871 atoms. Found 2 (6 requested) and removed 6 (3 requested) atoms. Cycle 10: After refmac, R = 0.3204 (Rfree = 0.000) for 866 atoms. Found 5 (6 requested) and removed 8 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.71 3.02 Search for helices and strands: 0 residues in 0 chains, 882 seeds are put forward NCS extension: 0 residues added, 882 seeds are put forward Round 1: 49 peptides, 9 chains. Longest chain 9 peptides. Score 0.345 Round 2: 49 peptides, 9 chains. Longest chain 9 peptides. Score 0.345 Round 3: 42 peptides, 9 chains. Longest chain 6 peptides. Score 0.253 Round 4: 53 peptides, 10 chains. Longest chain 9 peptides. Score 0.342 Round 5: 55 peptides, 9 chains. Longest chain 11 peptides. Score 0.418 Taking the results from Round 5 Chains 9, Residues 46, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2008 reflections ( 98.14 % complete ) and 2054 restraints for refining 891 atoms. 1879 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3290 (Rfree = 0.000) for 891 atoms. Found 6 (6 requested) and removed 18 (3 requested) atoms. Cycle 12: After refmac, R = 0.3407 (Rfree = 0.000) for 873 atoms. Found 6 (6 requested) and removed 11 (3 requested) atoms. Cycle 13: After refmac, R = 0.3582 (Rfree = 0.000) for 865 atoms. Found 6 (6 requested) and removed 14 (3 requested) atoms. Cycle 14: After refmac, R = 0.3650 (Rfree = 0.000) for 847 atoms. Found 6 (6 requested) and removed 11 (3 requested) atoms. Cycle 15: After refmac, R = 0.3424 (Rfree = 0.000) for 841 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.03 3.37 Search for helices and strands: 0 residues in 0 chains, 880 seeds are put forward NCS extension: 0 residues added, 880 seeds are put forward Round 1: 54 peptides, 12 chains. Longest chain 6 peptides. Score 0.248 Round 2: 59 peptides, 11 chains. Longest chain 8 peptides. Score 0.364 Round 3: 65 peptides, 12 chains. Longest chain 9 peptides. Score 0.385 Round 4: 63 peptides, 9 chains. Longest chain 12 peptides. Score 0.506 Round 5: 59 peptides, 10 chains. Longest chain 9 peptides. Score 0.414 Taking the results from Round 4 Chains 9, Residues 54, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2008 reflections ( 98.14 % complete ) and 1791 restraints for refining 839 atoms. 1584 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3589 (Rfree = 0.000) for 839 atoms. Found 6 (6 requested) and removed 22 (3 requested) atoms. Cycle 17: After refmac, R = 0.3157 (Rfree = 0.000) for 816 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. Cycle 18: After refmac, R = 0.3346 (Rfree = 0.000) for 811 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. Cycle 19: After refmac, R = 0.3040 (Rfree = 0.000) for 806 atoms. Found 5 (6 requested) and removed 4 (3 requested) atoms. Cycle 20: After refmac, R = 0.2937 (Rfree = 0.000) for 805 atoms. Found 0 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.56 3.96 Search for helices and strands: 0 residues in 0 chains, 836 seeds are put forward NCS extension: 0 residues added, 836 seeds are put forward Round 1: 51 peptides, 10 chains. Longest chain 8 peptides. Score 0.317 Round 2: 69 peptides, 13 chains. Longest chain 8 peptides. Score 0.382 Round 3: 71 peptides, 12 chains. Longest chain 13 peptides. Score 0.452 Round 4: 68 peptides, 11 chains. Longest chain 12 peptides. Score 0.466 Round 5: 62 peptides, 11 chains. Longest chain 10 peptides. Score 0.399 Taking the results from Round 4 Chains 11, Residues 57, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2008 reflections ( 98.14 % complete ) and 1751 restraints for refining 832 atoms. 1534 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3928 (Rfree = 0.000) for 832 atoms. Found 6 (6 requested) and removed 17 (3 requested) atoms. Cycle 22: After refmac, R = 0.3417 (Rfree = 0.000) for 815 atoms. Found 5 (6 requested) and removed 19 (3 requested) atoms. Cycle 23: After refmac, R = 0.3277 (Rfree = 0.000) for 795 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 24: After refmac, R = 0.3196 (Rfree = 0.000) for 791 atoms. Found 2 (6 requested) and removed 4 (3 requested) atoms. Cycle 25: After refmac, R = 0.3223 (Rfree = 0.000) for 789 atoms. Found 2 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.57 3.98 Search for helices and strands: 0 residues in 0 chains, 809 seeds are put forward NCS extension: 0 residues added, 809 seeds are put forward Round 1: 48 peptides, 9 chains. Longest chain 13 peptides. Score 0.333 Round 2: 56 peptides, 10 chains. Longest chain 10 peptides. Score 0.379 Round 3: 63 peptides, 11 chains. Longest chain 13 peptides. Score 0.411 Round 4: 61 peptides, 9 chains. Longest chain 19 peptides. Score 0.485 Round 5: 42 peptides, 6 chains. Longest chain 16 peptides. Score 0.422 Taking the results from Round 4 Chains 9, Residues 52, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2008 reflections ( 98.14 % complete ) and 1665 restraints for refining 801 atoms. 1466 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3600 (Rfree = 0.000) for 801 atoms. Found 6 (6 requested) and removed 13 (3 requested) atoms. Cycle 27: After refmac, R = 0.3452 (Rfree = 0.000) for 788 atoms. Found 4 (5 requested) and removed 4 (2 requested) atoms. Cycle 28: After refmac, R = 0.3410 (Rfree = 0.000) for 786 atoms. Found 4 (5 requested) and removed 5 (2 requested) atoms. Cycle 29: After refmac, R = 0.3592 (Rfree = 0.000) for 782 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. Cycle 30: After refmac, R = 0.3617 (Rfree = 0.000) for 777 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.70 4.12 Search for helices and strands: 0 residues in 0 chains, 790 seeds are put forward NCS extension: 0 residues added, 790 seeds are put forward Round 1: 46 peptides, 9 chains. Longest chain 10 peptides. Score 0.307 Round 2: 58 peptides, 10 chains. Longest chain 13 peptides. Score 0.402 Round 3: 58 peptides, 11 chains. Longest chain 8 peptides. Score 0.352 Round 4: 56 peptides, 10 chains. Longest chain 9 peptides. Score 0.379 Round 5: 65 peptides, 10 chains. Longest chain 12 peptides. Score 0.480 Taking the results from Round 5 Chains 10, Residues 55, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2008 reflections ( 98.14 % complete ) and 1680 restraints for refining 824 atoms. 1470 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3448 (Rfree = 0.000) for 824 atoms. Found 4 (6 requested) and removed 11 (3 requested) atoms. Cycle 32: After refmac, R = 0.3366 (Rfree = 0.000) for 814 atoms. Found 3 (6 requested) and removed 7 (3 requested) atoms. Cycle 33: After refmac, R = 0.3476 (Rfree = 0.000) for 810 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 34: After refmac, R = 0.3349 (Rfree = 0.000) for 804 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. Cycle 35: After refmac, R = 0.3213 (Rfree = 0.000) for 799 atoms. Found 1 (6 requested) and removed 8 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.57 3.98 Search for helices and strands: 0 residues in 0 chains, 816 seeds are put forward NCS extension: 0 residues added, 816 seeds are put forward Round 1: 42 peptides, 9 chains. Longest chain 7 peptides. Score 0.253 Round 2: 48 peptides, 8 chains. Longest chain 11 peptides. Score 0.387 Round 3: 51 peptides, 8 chains. Longest chain 11 peptides. Score 0.423 Round 4: 53 peptides, 10 chains. Longest chain 10 peptides. Score 0.342 Round 5: 56 peptides, 9 chains. Longest chain 12 peptides. Score 0.429 Taking the results from Round 5 Chains 9, Residues 47, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2008 reflections ( 98.14 % complete ) and 1807 restraints for refining 852 atoms. 1628 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3475 (Rfree = 0.000) for 852 atoms. Found 5 (6 requested) and removed 13 (3 requested) atoms. Cycle 37: After refmac, R = 0.3560 (Rfree = 0.000) for 843 atoms. Found 6 (6 requested) and removed 13 (3 requested) atoms. Cycle 38: After refmac, R = 0.3426 (Rfree = 0.000) for 833 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. Cycle 39: After refmac, R = 0.3558 (Rfree = 0.000) for 829 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. Cycle 40: After refmac, R = 0.3230 (Rfree = 0.000) for 824 atoms. Found 3 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 4.06 4.52 Search for helices and strands: 0 residues in 0 chains, 846 seeds are put forward NCS extension: 0 residues added, 846 seeds are put forward Round 1: 46 peptides, 10 chains. Longest chain 7 peptides. Score 0.251 Round 2: 61 peptides, 11 chains. Longest chain 10 peptides. Score 0.387 Round 3: 59 peptides, 10 chains. Longest chain 12 peptides. Score 0.414 Round 4: 56 peptides, 8 chains. Longest chain 16 peptides. Score 0.479 Round 5: 63 peptides, 10 chains. Longest chain 14 peptides. Score 0.459 Taking the results from Round 4 Chains 8, Residues 48, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2008 reflections ( 98.14 % complete ) and 1778 restraints for refining 840 atoms. 1594 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3389 (Rfree = 0.000) for 840 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. Cycle 42: After refmac, R = 0.3256 (Rfree = 0.000) for 838 atoms. Found 2 (6 requested) and removed 10 (3 requested) atoms. Cycle 43: After refmac, R = 0.3168 (Rfree = 0.000) for 830 atoms. Found 1 (6 requested) and removed 4 (3 requested) atoms. Cycle 44: After refmac, R = 0.3168 (Rfree = 0.000) for 825 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 45: After refmac, R = 0.3171 (Rfree = 0.000) for 819 atoms. Found 0 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.69 4.11 Search for helices and strands: 0 residues in 0 chains, 829 seeds are put forward NCS extension: 0 residues added, 829 seeds are put forward Round 1: 46 peptides, 10 chains. Longest chain 9 peptides. Score 0.251 Round 2: 55 peptides, 9 chains. Longest chain 11 peptides. Score 0.418 Round 3: 49 peptides, 9 chains. Longest chain 9 peptides. Score 0.345 Round 4: 52 peptides, 8 chains. Longest chain 12 peptides. Score 0.434 Round 5: 59 peptides, 10 chains. Longest chain 16 peptides. Score 0.414 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 8, Residues 44, 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 1vpz-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2008 reflections ( 98.14 % complete ) and 1790 restraints for refining 840 atoms. 1622 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3222 (Rfree = 0.000) for 840 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.3201 (Rfree = 0.000) for 836 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.3170 (Rfree = 0.000) for 831 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.3342 (Rfree = 0.000) for 824 atoms. TimeTaking 18.23