Sun 23 Dec 22:22:56 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 1vr8-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vr8-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vr8-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vr8-3.4-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/1vr8-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vr8-3.4-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 22:23:05 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/1vr8-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vr8-3.4-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 122 and 0 Target number of residues in the AU: 122 Target solvent content: 0.6104 Checking the provided sequence file Detected sequence length: 142 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 142 Adjusted target solvent content: 0.55 Input MTZ file: 1vr8-3.4-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: 154 Cell parameters: 57.762 57.762 87.976 90.000 90.000 120.000 Input sequence file: 1vr8-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 1136 target number of atoms Had to go as low as 0.80 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: 50.023 3.402 Wilson plot Bfac: 56.02 2535 reflections ( 99.76 % complete ) and 0 restraints for refining 1269 atoms. Observations/parameters ratio is 0.50 ------------------------------------------------------ Starting model: R = 0.3277 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3341 (Rfree = 0.000) for 1269 atoms. Found 9 (9 requested) and removed 31 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.16 2.96 Search for helices and strands: 0 residues in 0 chains, 1270 seeds are put forward Round 1: 75 peptides, 14 chains. Longest chain 9 peptides. Score 0.366 Round 2: 95 peptides, 12 chains. Longest chain 17 peptides. Score 0.605 Round 3: 102 peptides, 10 chains. Longest chain 25 peptides. Score 0.705 Round 4: 101 peptides, 12 chains. Longest chain 19 peptides. Score 0.645 Round 5: 99 peptides, 10 chains. Longest chain 19 peptides. Score 0.688 Taking the results from Round 3 Chains 11, Residues 92, Estimated correctness of the model 59.1 % 2 chains (31 residues) have been docked in sequence Building loops using Loopy2018 11 chains (92 residues) following loop building 2 chains (31 residues) in sequence following loop building ------------------------------------------------------ 2535 reflections ( 99.76 % complete ) and 1909 restraints for refining 1033 atoms. 1432 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3062 (Rfree = 0.000) for 1033 atoms. Found 7 (7 requested) and removed 11 (3 requested) atoms. Cycle 2: After refmac, R = 0.2892 (Rfree = 0.000) for 1000 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 3: After refmac, R = 0.2739 (Rfree = 0.000) for 985 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 4: After refmac, R = 0.2534 (Rfree = 0.000) for 980 atoms. Found 6 (7 requested) and removed 6 (3 requested) atoms. Cycle 5: After refmac, R = 0.2633 (Rfree = 0.000) for 977 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.10 2.90 Search for helices and strands: 0 residues in 0 chains, 1011 seeds are put forward Round 1: 84 peptides, 14 chains. Longest chain 11 peptides. Score 0.449 Round 2: 85 peptides, 11 chains. Longest chain 18 peptides. Score 0.565 Round 3: 101 peptides, 11 chains. Longest chain 27 peptides. Score 0.673 Round 4: 96 peptides, 10 chains. Longest chain 21 peptides. Score 0.671 Round 5: 98 peptides, 11 chains. Longest chain 18 peptides. Score 0.654 Taking the results from Round 3 Chains 11, Residues 90, Estimated correctness of the model 50.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2535 reflections ( 99.76 % complete ) and 2224 restraints for refining 1032 atoms. 1875 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2785 (Rfree = 0.000) for 1032 atoms. Found 6 (6 requested) and removed 28 (3 requested) atoms. Cycle 7: After refmac, R = 0.2838 (Rfree = 0.000) for 999 atoms. Found 6 (6 requested) and removed 20 (3 requested) atoms. Cycle 8: After refmac, R = 0.3024 (Rfree = 0.000) for 980 atoms. Found 6 (6 requested) and removed 10 (3 requested) atoms. Cycle 9: After refmac, R = 0.2468 (Rfree = 0.000) for 975 atoms. Found 0 (6 requested) and removed 7 (3 requested) atoms. Cycle 10: After refmac, R = 0.2477 (Rfree = 0.000) for 966 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.14 2.94 Search for helices and strands: 0 residues in 0 chains, 998 seeds are put forward Round 1: 75 peptides, 15 chains. Longest chain 8 peptides. Score 0.325 Round 2: 82 peptides, 14 chains. Longest chain 14 peptides. Score 0.431 Round 3: 79 peptides, 12 chains. Longest chain 19 peptides. Score 0.481 Round 4: 89 peptides, 11 chains. Longest chain 27 peptides. Score 0.594 Round 5: 91 peptides, 13 chains. Longest chain 12 peptides. Score 0.543 Taking the results from Round 4 Chains 11, Residues 78, Estimated correctness of the model 26.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2535 reflections ( 99.76 % complete ) and 2231 restraints for refining 1021 atoms. 1930 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3214 (Rfree = 0.000) for 1021 atoms. Found 6 (6 requested) and removed 12 (3 requested) atoms. Cycle 12: After refmac, R = 0.3092 (Rfree = 0.000) for 1010 atoms. Found 6 (6 requested) and removed 15 (3 requested) atoms. Cycle 13: After refmac, R = 0.2928 (Rfree = 0.000) for 996 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 14: After refmac, R = 0.3096 (Rfree = 0.000) for 995 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. Cycle 15: After refmac, R = 0.3138 (Rfree = 0.000) for 986 atoms. Found 6 (6 requested) and removed 10 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.18 2.97 Search for helices and strands: 0 residues in 0 chains, 1011 seeds are put forward Round 1: 85 peptides, 13 chains. Longest chain 20 peptides. Score 0.495 Round 2: 90 peptides, 12 chains. Longest chain 28 peptides. Score 0.569 Round 3: 95 peptides, 12 chains. Longest chain 17 peptides. Score 0.605 Round 4: 89 peptides, 13 chains. Longest chain 13 peptides. Score 0.527 Round 5: 100 peptides, 13 chains. Longest chain 17 peptides. Score 0.608 Taking the results from Round 5 Chains 13, Residues 87, Estimated correctness of the model 31.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2535 reflections ( 99.76 % complete ) and 2262 restraints for refining 1033 atoms. 1927 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3104 (Rfree = 0.000) for 1033 atoms. Found 6 (6 requested) and removed 11 (3 requested) atoms. Cycle 17: After refmac, R = 0.3010 (Rfree = 0.000) for 1016 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 18: After refmac, R = 0.3035 (Rfree = 0.000) for 1013 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 19: After refmac, R = 0.3095 (Rfree = 0.000) for 1010 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 20: After refmac, R = 0.3492 (Rfree = 0.000) for 1007 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.27 3.06 Search for helices and strands: 0 residues in 0 chains, 1069 seeds are put forward Round 1: 69 peptides, 12 chains. Longest chain 12 peptides. Score 0.391 Round 2: 77 peptides, 14 chains. Longest chain 11 peptides. Score 0.385 Round 3: 70 peptides, 11 chains. Longest chain 15 peptides. Score 0.440 Round 4: 70 peptides, 12 chains. Longest chain 9 peptides. Score 0.400 Round 5: 76 peptides, 11 chains. Longest chain 17 peptides. Score 0.493 Taking the results from Round 5 Chains 11, Residues 65, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2535 reflections ( 99.76 % complete ) and 2338 restraints for refining 1033 atoms. 2089 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3271 (Rfree = 0.000) for 1033 atoms. Found 6 (6 requested) and removed 11 (3 requested) atoms. Cycle 22: After refmac, R = 0.3199 (Rfree = 0.000) for 1019 atoms. Found 4 (6 requested) and removed 8 (3 requested) atoms. Cycle 23: After refmac, R = 0.3466 (Rfree = 0.000) for 1004 atoms. Found 6 (6 requested) and removed 17 (3 requested) atoms. Cycle 24: After refmac, R = 0.3266 (Rfree = 0.000) for 989 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. Cycle 25: After refmac, R = 0.3586 (Rfree = 0.000) for 977 atoms. Found 6 (6 requested) and removed 14 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.79 3.55 Search for helices and strands: 0 residues in 0 chains, 1028 seeds are put forward Round 1: 63 peptides, 14 chains. Longest chain 6 peptides. Score 0.244 Round 2: 72 peptides, 14 chains. Longest chain 8 peptides. Score 0.337 Round 3: 73 peptides, 12 chains. Longest chain 10 peptides. Score 0.428 Round 4: 80 peptides, 14 chains. Longest chain 13 peptides. Score 0.413 Round 5: 75 peptides, 11 chains. Longest chain 18 peptides. Score 0.484 Taking the results from Round 5 Chains 11, Residues 64, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2535 reflections ( 99.76 % complete ) and 2336 restraints for refining 1033 atoms. 2091 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3145 (Rfree = 0.000) for 1033 atoms. Found 6 (6 requested) and removed 10 (3 requested) atoms. Cycle 27: After refmac, R = 0.3872 (Rfree = 0.000) for 1023 atoms. Found 6 (6 requested) and removed 25 (3 requested) atoms. Cycle 28: After refmac, R = 0.3375 (Rfree = 0.000) for 990 atoms. Found 6 (6 requested) and removed 10 (3 requested) atoms. Cycle 29: After refmac, R = 0.3209 (Rfree = 0.000) for 978 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. Cycle 30: After refmac, R = 0.3469 (Rfree = 0.000) for 968 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.37 3.15 Search for helices and strands: 0 residues in 0 chains, 1010 seeds are put forward Round 1: 63 peptides, 12 chains. Longest chain 9 peptides. Score 0.331 Round 2: 75 peptides, 10 chains. Longest chain 16 peptides. Score 0.522 Round 3: 77 peptides, 12 chains. Longest chain 11 peptides. Score 0.464 Round 4: 73 peptides, 11 chains. Longest chain 15 peptides. Score 0.467 Round 5: 76 peptides, 11 chains. Longest chain 17 peptides. Score 0.493 Taking the results from Round 2 Chains 10, Residues 65, Estimated correctness of the model 1.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2535 reflections ( 99.76 % complete ) and 2126 restraints for refining 984 atoms. 1876 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3307 (Rfree = 0.000) for 984 atoms. Found 6 (6 requested) and removed 12 (3 requested) atoms. Cycle 32: After refmac, R = 0.3247 (Rfree = 0.000) for 959 atoms. Found 6 (6 requested) and removed 24 (3 requested) atoms. Cycle 33: After refmac, R = 0.3044 (Rfree = 0.000) for 937 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. Cycle 34: After refmac, R = 0.2984 (Rfree = 0.000) for 932 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 35: After refmac, R = 0.3616 (Rfree = 0.000) for 929 atoms. Found 6 (6 requested) and removed 14 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.29 3.08 Search for helices and strands: 0 residues in 0 chains, 960 seeds are put forward Round 1: 56 peptides, 10 chains. Longest chain 12 peptides. Score 0.347 Round 2: 70 peptides, 11 chains. Longest chain 10 peptides. Score 0.440 Round 3: 66 peptides, 12 chains. Longest chain 10 peptides. Score 0.361 Round 4: 74 peptides, 14 chains. Longest chain 12 peptides. Score 0.357 Round 5: 64 peptides, 12 chains. Longest chain 8 peptides. Score 0.342 Taking the results from Round 2 Chains 11, Residues 59, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2535 reflections ( 99.76 % complete ) and 2144 restraints for refining 985 atoms. 1919 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3270 (Rfree = 0.000) for 985 atoms. Found 6 (6 requested) and removed 14 (3 requested) atoms. Cycle 37: After refmac, R = 0.3058 (Rfree = 0.000) for 968 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 38: After refmac, R = 0.3087 (Rfree = 0.000) for 968 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 39: After refmac, R = 0.3376 (Rfree = 0.000) for 967 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 40: After refmac, R = 0.3095 (Rfree = 0.000) for 954 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.44 3.22 Search for helices and strands: 0 residues in 0 chains, 983 seeds are put forward Round 1: 47 peptides, 10 chains. Longest chain 8 peptides. Score 0.250 Round 2: 56 peptides, 11 chains. Longest chain 7 peptides. Score 0.303 Round 3: 47 peptides, 9 chains. Longest chain 10 peptides. Score 0.298 Round 4: 45 peptides, 8 chains. Longest chain 8 peptides. Score 0.324 Round 5: 47 peptides, 8 chains. Longest chain 11 peptides. Score 0.345 Taking the results from Round 5 Chains 8, Residues 39, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2535 reflections ( 99.76 % complete ) and 2309 restraints for refining 997 atoms. 2161 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3347 (Rfree = 0.000) for 997 atoms. Found 6 (6 requested) and removed 12 (3 requested) atoms. Cycle 42: After refmac, R = 0.3186 (Rfree = 0.000) for 988 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. Cycle 43: After refmac, R = 0.3584 (Rfree = 0.000) for 983 atoms. Found 6 (6 requested) and removed 13 (3 requested) atoms. Cycle 44: After refmac, R = 0.3160 (Rfree = 0.000) for 974 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 45: After refmac, R = 0.3092 (Rfree = 0.000) for 969 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.27 3.06 Search for helices and strands: 0 residues in 0 chains, 989 seeds are put forward Round 1: 33 peptides, 7 chains. Longest chain 6 peptides. Score 0.234 Round 2: 36 peptides, 7 chains. Longest chain 10 peptides. Score 0.271 Round 3: 43 peptides, 8 chains. Longest chain 8 peptides. Score 0.302 Round 4: 51 peptides, 8 chains. Longest chain 12 peptides. Score 0.386 Round 5: 48 peptides, 9 chains. Longest chain 9 peptides. Score 0.309 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 8, Residues 43, 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 1vr8-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2535 reflections ( 99.76 % complete ) and 2036 restraints for refining 919 atoms. 1872 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3347 (Rfree = 0.000) for 919 atoms. Found 0 (5 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.3467 (Rfree = 0.000) for 908 atoms. Found 0 (5 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.3570 (Rfree = 0.000) for 902 atoms. Found 0 (5 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.3684 (Rfree = 0.000) for 895 atoms. TimeTaking 25.07