Sun 23 Dec 22:22:43 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 2ets-2.3-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ets-2.3-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ets-2.3-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ets-2.3-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/2ets-2.3-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ets-2.3-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 22:22:53 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/2ets-2.3-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ets-2.3-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 139 and 0 Target number of residues in the AU: 139 Target solvent content: 0.5578 Checking the provided sequence file Detected sequence length: 128 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 128 Adjusted target solvent content: 0.59 Input MTZ file: 2ets-2.3-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: 155 Cell parameters: 93.473 93.473 101.164 90.000 90.000 120.000 Input sequence file: 2ets-2.3-parrot-hancs.fasta_lf Building free atoms model in initial map for 1024 target number of atoms Had to go as low as 0.65 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 1 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: 63.206 2.251 Wilson plot Bfac: 37.63 8245 reflections ( 99.90 % complete ) and 0 restraints for refining 1139 atoms. Observations/parameters ratio is 1.81 ------------------------------------------------------ Starting model: R = 0.3819 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3373 (Rfree = 0.000) for 1139 atoms. Found 21 (27 requested) and removed 18 (13 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.50 2.21 Round 1: 83 peptides, 12 chains. Longest chain 16 peptides. Score 0.514 Round 2: 80 peptides, 9 chains. Longest chain 28 peptides. Score 0.595 Round 3: 82 peptides, 7 chains. Longest chain 33 peptides. Score 0.672 Round 4: 90 peptides, 9 chains. Longest chain 26 peptides. Score 0.663 Round 5: 87 peptides, 7 chains. Longest chain 50 peptides. Score 0.702 Taking the results from Round 5 Chains 7, Residues 80, Estimated correctness of the model 88.7 % 1 chains (49 residues) have been docked in sequence ------------------------------------------------------ 8245 reflections ( 99.90 % complete ) and 1551 restraints for refining 986 atoms. 1016 conditional restraints added. Observations/parameters ratio is 2.09 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3648 (Rfree = 0.000) for 986 atoms. Found 18 (24 requested) and removed 13 (12 requested) atoms. Cycle 2: After refmac, R = 0.3451 (Rfree = 0.000) for 981 atoms. Found 19 (24 requested) and removed 12 (12 requested) atoms. Cycle 3: After refmac, R = 0.3339 (Rfree = 0.000) for 981 atoms. Found 19 (23 requested) and removed 13 (12 requested) atoms. Cycle 4: After refmac, R = 0.3168 (Rfree = 0.000) for 982 atoms. Found 18 (23 requested) and removed 12 (12 requested) atoms. Cycle 5: After refmac, R = 0.3058 (Rfree = 0.000) for 983 atoms. Found 13 (22 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.43 2.15 Round 1: 83 peptides, 7 chains. Longest chain 54 peptides. Score 0.678 Round 2: 93 peptides, 7 chains. Longest chain 47 peptides. Score 0.734 Round 3: 102 peptides, 8 chains. Longest chain 43 peptides. Score 0.754 Round 4: 96 peptides, 6 chains. Longest chain 51 peptides. Score 0.773 Round 5: 103 peptides, 7 chains. Longest chain 47 peptides. Score 0.781 Taking the results from Round 5 Chains 7, Residues 96, Estimated correctness of the model 93.6 % 1 chains (46 residues) have been docked in sequence ------------------------------------------------------ 8245 reflections ( 99.90 % complete ) and 1462 restraints for refining 974 atoms. 872 conditional restraints added. Observations/parameters ratio is 2.12 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3302 (Rfree = 0.000) for 974 atoms. Found 21 (21 requested) and removed 14 (11 requested) atoms. Cycle 7: After refmac, R = 0.3091 (Rfree = 0.000) for 980 atoms. Found 20 (20 requested) and removed 11 (11 requested) atoms. Cycle 8: After refmac, R = 0.2957 (Rfree = 0.000) for 985 atoms. Found 16 (21 requested) and removed 12 (12 requested) atoms. Cycle 9: After refmac, R = 0.2897 (Rfree = 0.000) for 988 atoms. Found 14 (20 requested) and removed 12 (12 requested) atoms. Cycle 10: After refmac, R = 0.2809 (Rfree = 0.000) for 990 atoms. Found 15 (20 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.42 2.14 Round 1: 94 peptides, 5 chains. Longest chain 55 peptides. Score 0.787 Round 2: 94 peptides, 4 chains. Longest chain 58 peptides. Score 0.809 Round 3: 97 peptides, 5 chains. Longest chain 45 peptides. Score 0.800 Round 4: 103 peptides, 5 chains. Longest chain 51 peptides. Score 0.822 Round 5: 103 peptides, 4 chains. Longest chain 51 peptides. Score 0.841 Taking the results from Round 5 Chains 4, Residues 99, Estimated correctness of the model 96.4 % 2 chains (86 residues) have been docked in sequence Building loops using Loopy2018 4 chains (99 residues) following loop building 2 chains (86 residues) in sequence following loop building ------------------------------------------------------ 8245 reflections ( 99.90 % complete ) and 1125 restraints for refining 1003 atoms. 333 conditional restraints added. Observations/parameters ratio is 2.06 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3095 (Rfree = 0.000) for 1003 atoms. Found 19 (19 requested) and removed 14 (12 requested) atoms. Cycle 12: After refmac, R = 0.2918 (Rfree = 0.000) for 1002 atoms. Found 19 (19 requested) and removed 12 (12 requested) atoms. Cycle 13: After refmac, R = 0.2757 (Rfree = 0.000) for 1007 atoms. Found 18 (18 requested) and removed 12 (12 requested) atoms. Cycle 14: After refmac, R = 0.2663 (Rfree = 0.000) for 1010 atoms. Found 13 (18 requested) and removed 12 (12 requested) atoms. Cycle 15: After refmac, R = 0.2578 (Rfree = 0.000) for 1010 atoms. Found 16 (17 requested) and removed 8 (12 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.39 2.12 Round 1: 101 peptides, 4 chains. Longest chain 49 peptides. Score 0.835 Round 2: 99 peptides, 5 chains. Longest chain 40 peptides. Score 0.807 Round 3: 102 peptides, 2 chains. Longest chain 96 peptides. Score 0.874 Round 4: 103 peptides, 3 chains. Longest chain 69 peptides. Score 0.860 Round 5: 101 peptides, 5 chains. Longest chain 49 peptides. Score 0.815 Taking the results from Round 3 Chains 2, Residues 100, Estimated correctness of the model 97.7 % 1 chains (95 residues) have been docked in sequence ------------------------------------------------------ 8245 reflections ( 99.90 % complete ) and 1065 restraints for refining 1015 atoms. 213 conditional restraints added. Observations/parameters ratio is 2.03 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2820 (Rfree = 0.000) for 1015 atoms. Found 17 (17 requested) and removed 15 (12 requested) atoms. Cycle 17: After refmac, R = 0.2594 (Rfree = 0.000) for 1015 atoms. Found 17 (17 requested) and removed 12 (12 requested) atoms. Cycle 18: After refmac, R = 0.2537 (Rfree = 0.000) for 1017 atoms. Found 16 (16 requested) and removed 12 (12 requested) atoms. Cycle 19: After refmac, R = 0.2448 (Rfree = 0.000) for 1020 atoms. Found 16 (16 requested) and removed 12 (12 requested) atoms. Cycle 20: After refmac, R = 0.2403 (Rfree = 0.000) for 1021 atoms. Found 16 (16 requested) and removed 7 (12 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.37 2.10 Round 1: 101 peptides, 4 chains. Longest chain 75 peptides. Score 0.835 Round 2: 99 peptides, 5 chains. Longest chain 31 peptides. Score 0.807 Round 3: 103 peptides, 4 chains. Longest chain 47 peptides. Score 0.841 Round 4: 105 peptides, 5 chains. Longest chain 57 peptides. Score 0.829 Round 5: 102 peptides, 5 chains. Longest chain 65 peptides. Score 0.819 Taking the results from Round 3 Chains 4, Residues 99, Estimated correctness of the model 96.4 % 2 chains (87 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 67 A and 70 A 3 chains (101 residues) following loop building 1 chains (89 residues) in sequence following loop building ------------------------------------------------------ 8245 reflections ( 99.90 % complete ) and 1110 restraints for refining 1010 atoms. 286 conditional restraints added. Observations/parameters ratio is 2.04 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2758 (Rfree = 0.000) for 1010 atoms. Found 15 (15 requested) and removed 13 (12 requested) atoms. Cycle 22: After refmac, R = 0.2553 (Rfree = 0.000) for 1010 atoms. Found 15 (15 requested) and removed 8 (12 requested) atoms. Cycle 23: After refmac, R = 0.2473 (Rfree = 0.000) for 1016 atoms. Found 14 (14 requested) and removed 10 (12 requested) atoms. Cycle 24: After refmac, R = 0.2401 (Rfree = 0.000) for 1018 atoms. Found 14 (14 requested) and removed 5 (12 requested) atoms. Cycle 25: After refmac, R = 0.2356 (Rfree = 0.000) for 1027 atoms. Found 13 (14 requested) and removed 4 (12 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.37 2.10 Round 1: 103 peptides, 1 chains. Longest chain 103 peptides. Score 0.893 Round 2: 100 peptides, 5 chains. Longest chain 46 peptides. Score 0.811 Round 3: 105 peptides, 4 chains. Longest chain 56 peptides. Score 0.848 Round 4: 101 peptides, 6 chains. Longest chain 26 peptides. Score 0.794 Round 5: 108 peptides, 3 chains. Longest chain 64 peptides. Score 0.874 Taking the results from Round 1 Chains 1, Residues 102, Estimated correctness of the model 98.3 % 1 chains (102 residues) have been docked in sequence ------------------------------------------------------ 8245 reflections ( 99.90 % complete ) and 1011 restraints for refining 1022 atoms. 124 conditional restraints added. Observations/parameters ratio is 2.02 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2481 (Rfree = 0.000) for 1022 atoms. Found 14 (14 requested) and removed 13 (12 requested) atoms. Cycle 27: After refmac, R = 0.2366 (Rfree = 0.000) for 1023 atoms. Found 13 (13 requested) and removed 12 (12 requested) atoms. Cycle 28: After refmac, R = 0.2285 (Rfree = 0.000) for 1023 atoms. Found 13 (13 requested) and removed 6 (12 requested) atoms. Cycle 29: After refmac, R = 0.2246 (Rfree = 0.000) for 1029 atoms. Found 13 (13 requested) and removed 8 (12 requested) atoms. Cycle 30: After refmac, R = 0.2249 (Rfree = 0.000) for 1034 atoms. Found 13 (13 requested) and removed 11 (12 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.37 2.10 Round 1: 103 peptides, 2 chains. Longest chain 96 peptides. Score 0.877 Round 2: 102 peptides, 4 chains. Longest chain 31 peptides. Score 0.838 Round 3: 100 peptides, 3 chains. Longest chain 54 peptides. Score 0.850 Round 4: 102 peptides, 6 chains. Longest chain 41 peptides. Score 0.798 Round 5: 104 peptides, 3 chains. Longest chain 85 peptides. Score 0.862 Taking the results from Round 1 Chains 2, Residues 101, Estimated correctness of the model 97.8 % 1 chains (95 residues) have been docked in sequence ------------------------------------------------------ 8245 reflections ( 99.90 % complete ) and 1095 restraints for refining 1023 atoms. 247 conditional restraints added. Observations/parameters ratio is 2.01 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2476 (Rfree = 0.000) for 1023 atoms. Found 12 (12 requested) and removed 12 (12 requested) atoms. Cycle 32: After refmac, R = 0.2342 (Rfree = 0.000) for 1022 atoms. Found 12 (12 requested) and removed 7 (12 requested) atoms. Cycle 33: After refmac, R = 0.2290 (Rfree = 0.000) for 1027 atoms. Found 12 (12 requested) and removed 6 (12 requested) atoms. Cycle 34: After refmac, R = 0.2273 (Rfree = 0.000) for 1033 atoms. Found 12 (12 requested) and removed 11 (12 requested) atoms. Cycle 35: After refmac, R = 0.2267 (Rfree = 0.000) for 1034 atoms. Found 12 (12 requested) and removed 8 (12 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.37 2.10 Round 1: 101 peptides, 3 chains. Longest chain 67 peptides. Score 0.853 Round 2: 103 peptides, 2 chains. Longest chain 75 peptides. Score 0.877 Round 3: 102 peptides, 3 chains. Longest chain 51 peptides. Score 0.857 Round 4: 94 peptides, 5 chains. Longest chain 44 peptides. Score 0.787 Round 5: 95 peptides, 4 chains. Longest chain 51 peptides. Score 0.813 Taking the results from Round 2 Chains 2, Residues 101, Estimated correctness of the model 97.8 % 2 chains (101 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 89 A and 92 A 1 chains (103 residues) following loop building 1 chains (103 residues) in sequence following loop building ------------------------------------------------------ 8245 reflections ( 99.90 % complete ) and 1000 restraints for refining 1019 atoms. 105 conditional restraints added. Observations/parameters ratio is 2.02 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2500 (Rfree = 0.000) for 1019 atoms. Found 12 (12 requested) and removed 12 (12 requested) atoms. Cycle 37: After refmac, R = 0.2323 (Rfree = 0.000) for 1019 atoms. Found 12 (12 requested) and removed 12 (12 requested) atoms. Cycle 38: After refmac, R = 0.2282 (Rfree = 0.000) for 1019 atoms. Found 12 (12 requested) and removed 11 (12 requested) atoms. Cycle 39: After refmac, R = 0.2259 (Rfree = 0.000) for 1019 atoms. Found 12 (12 requested) and removed 12 (12 requested) atoms. Cycle 40: After refmac, R = 0.2237 (Rfree = 0.000) for 1019 atoms. Found 12 (12 requested) and removed 8 (12 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.35 2.08 Round 1: 101 peptides, 2 chains. Longest chain 51 peptides. Score 0.871 Round 2: 100 peptides, 5 chains. Longest chain 31 peptides. Score 0.811 Round 3: 102 peptides, 2 chains. Longest chain 51 peptides. Score 0.874 Round 4: 98 peptides, 5 chains. Longest chain 51 peptides. Score 0.803 Round 5: 101 peptides, 4 chains. Longest chain 37 peptides. Score 0.835 Taking the results from Round 3 Chains 2, Residues 100, Estimated correctness of the model 97.7 % 2 chains (100 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 66 A and 69 A 1 chains (102 residues) following loop building 1 chains (102 residues) in sequence following loop building ------------------------------------------------------ 8245 reflections ( 99.90 % complete ) and 1028 restraints for refining 1023 atoms. 141 conditional restraints added. Observations/parameters ratio is 2.01 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2468 (Rfree = 0.000) for 1023 atoms. Found 12 (12 requested) and removed 14 (12 requested) atoms. Cycle 42: After refmac, R = 0.2298 (Rfree = 0.000) for 1020 atoms. Found 12 (12 requested) and removed 10 (12 requested) atoms. Cycle 43: After refmac, R = 0.2264 (Rfree = 0.000) for 1022 atoms. Found 12 (12 requested) and removed 5 (12 requested) atoms. Cycle 44: After refmac, R = 0.2200 (Rfree = 0.000) for 1029 atoms. Found 12 (12 requested) and removed 10 (12 requested) atoms. Cycle 45: After refmac, R = 0.2198 (Rfree = 0.000) for 1031 atoms. Found 12 (12 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.36 2.09 Round 1: 102 peptides, 2 chains. Longest chain 51 peptides. Score 0.874 Round 2: 101 peptides, 4 chains. Longest chain 46 peptides. Score 0.835 Round 3: 102 peptides, 3 chains. Longest chain 51 peptides. Score 0.857 Round 4: 102 peptides, 3 chains. Longest chain 69 peptides. Score 0.857 Round 5: 100 peptides, 5 chains. Longest chain 44 peptides. Score 0.811 Taking the results from Round 1 Last building cycle: Chain fragments will be rearranged Chains 2, Residues 100, Estimated correctness of the model 97.7 % 2 chains (100 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 65 A and 68 A 1 chains (102 residues) following loop building 1 chains (102 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 8245 reflections ( 99.90 % complete ) and 887 restraints for refining 871 atoms. Observations/parameters ratio is 2.37 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2996 (Rfree = 0.000) for 871 atoms. Found 7 (10 requested) and removed 0 (10 requested) atoms. Cycle 47: After refmac, R = 0.2868 (Rfree = 0.000) for 871 atoms. Found 2 (10 requested) and removed 0 (10 requested) atoms. Cycle 48: After refmac, R = 0.2812 (Rfree = 0.000) for 871 atoms. Found 2 (10 requested) and removed 0 (10 requested) atoms. Cycle 49: After refmac, R = 0.2778 (Rfree = 0.000) for 871 atoms. TimeTaking 28.62