Sun 23 Dec 22:22:46 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 1vk9-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vk9-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vk9-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk9-4.0-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/1vk9-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk9-4.0-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 22:22:56 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/1vk9-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk9-4.0-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 206 and 0 Target number of residues in the AU: 206 Target solvent content: 0.6707 Checking the provided sequence file Detected sequence length: 151 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 151 Adjusted target solvent content: 0.76 Input MTZ file: 1vk9-4.0-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: 180 Cell parameters: 132.922 132.922 66.385 90.000 90.000 120.000 Input sequence file: 1vk9-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 1208 target number of atoms Had to go as low as 1.40 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: 115.114 4.002 Wilson plot Bfac: 93.09 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 3187 reflections ( 99.91 % complete ) and 0 restraints for refining 1520 atoms. Observations/parameters ratio is 0.52 ------------------------------------------------------ Starting model: R = 0.3604 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3295 (Rfree = 0.000) for 1520 atoms. Found 7 (7 requested) and removed 13 (3 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.97 2.70 Search for helices and strands: 0 residues in 0 chains, 1529 seeds are put forward Round 1: 97 peptides, 13 chains. Longest chain 12 peptides. Score 0.429 Round 2: 106 peptides, 10 chains. Longest chain 20 peptides. Score 0.534 Round 3: 110 peptides, 11 chains. Longest chain 26 peptides. Score 0.531 Round 4: 112 peptides, 12 chains. Longest chain 21 peptides. Score 0.519 Round 5: 108 peptides, 9 chains. Longest chain 27 peptides. Score 0.563 Taking the results from Round 5 Chains 10, Residues 99, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 3187 reflections ( 99.91 % complete ) and 2211 restraints for refining 1090 atoms. 1790 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3264 (Rfree = 0.000) for 1090 atoms. Found 5 (5 requested) and removed 8 (2 requested) atoms. Cycle 2: After refmac, R = 0.3253 (Rfree = 0.000) for 1057 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. Cycle 3: After refmac, R = 0.3144 (Rfree = 0.000) for 1050 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. Cycle 4: After refmac, R = 0.2950 (Rfree = 0.000) for 1042 atoms. Found 4 (4 requested) and removed 7 (2 requested) atoms. Cycle 5: After refmac, R = 0.3085 (Rfree = 0.000) for 1031 atoms. Found 4 (4 requested) and removed 6 (2 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.95 2.69 Search for helices and strands: 0 residues in 0 chains, 1081 seeds are put forward Round 1: 99 peptides, 12 chains. Longest chain 18 peptides. Score 0.461 Round 2: 102 peptides, 10 chains. Longest chain 24 peptides. Score 0.518 Round 3: 107 peptides, 10 chains. Longest chain 22 peptides. Score 0.539 Round 4: 102 peptides, 9 chains. Longest chain 33 peptides. Score 0.539 Round 5: 99 peptides, 12 chains. Longest chain 19 peptides. Score 0.461 Taking the results from Round 4 Chains 10, Residues 93, Estimated correctness of the model 0.0 % 2 chains (29 residues) have been docked in sequence ------------------------------------------------------ 3187 reflections ( 99.91 % complete ) and 2038 restraints for refining 1089 atoms. 1569 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3083 (Rfree = 0.000) for 1089 atoms. Found 5 (5 requested) and removed 6 (2 requested) atoms. Cycle 7: After refmac, R = 0.2811 (Rfree = 0.000) for 1080 atoms. Found 5 (5 requested) and removed 6 (2 requested) atoms. Cycle 8: After refmac, R = 0.2878 (Rfree = 0.000) for 1072 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 9: After refmac, R = 0.2759 (Rfree = 0.000) for 1065 atoms. Found 5 (5 requested) and removed 8 (2 requested) atoms. Cycle 10: After refmac, R = 0.2805 (Rfree = 0.000) for 1059 atoms. Found 5 (5 requested) and removed 8 (2 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.85 2.62 Search for helices and strands: 0 residues in 0 chains, 1112 seeds are put forward Round 1: 103 peptides, 13 chains. Longest chain 16 peptides. Score 0.458 Round 2: 114 peptides, 14 chains. Longest chain 22 peptides. Score 0.486 Round 3: 106 peptides, 12 chains. Longest chain 25 peptides. Score 0.493 Round 4: 105 peptides, 11 chains. Longest chain 21 peptides. Score 0.509 Round 5: 92 peptides, 9 chains. Longest chain 17 peptides. Score 0.496 Taking the results from Round 4 Chains 11, Residues 94, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3187 reflections ( 99.91 % complete ) and 2401 restraints for refining 1091 atoms. 2036 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2974 (Rfree = 0.000) for 1091 atoms. Found 5 (5 requested) and removed 10 (2 requested) atoms. Cycle 12: After refmac, R = 0.2853 (Rfree = 0.000) for 1080 atoms. Found 5 (5 requested) and removed 9 (2 requested) atoms. Cycle 13: After refmac, R = 0.2735 (Rfree = 0.000) for 1074 atoms. Found 5 (5 requested) and removed 6 (2 requested) atoms. Cycle 14: After refmac, R = 0.2675 (Rfree = 0.000) for 1071 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 15: After refmac, R = 0.2704 (Rfree = 0.000) for 1073 atoms. Found 5 (5 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.88 2.64 Search for helices and strands: 0 residues in 0 chains, 1125 seeds are put forward Round 1: 100 peptides, 10 chains. Longest chain 17 peptides. Score 0.509 Round 2: 104 peptides, 11 chains. Longest chain 16 peptides. Score 0.505 Round 3: 107 peptides, 11 chains. Longest chain 18 peptides. Score 0.518 Round 4: 111 peptides, 13 chains. Longest chain 18 peptides. Score 0.494 Round 5: 117 peptides, 11 chains. Longest chain 28 peptides. Score 0.559 Taking the results from Round 5 Chains 11, Residues 106, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3187 reflections ( 99.91 % complete ) and 2271 restraints for refining 1091 atoms. 1858 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2789 (Rfree = 0.000) for 1091 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. Cycle 17: After refmac, R = 0.2838 (Rfree = 0.000) for 1085 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 18: After refmac, R = 0.2756 (Rfree = 0.000) for 1080 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 19: After refmac, R = 0.2822 (Rfree = 0.000) for 1080 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. Cycle 20: After refmac, R = 0.2582 (Rfree = 0.000) for 1078 atoms. Found 5 (5 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.82 2.60 Search for helices and strands: 0 residues in 0 chains, 1144 seeds are put forward Round 1: 102 peptides, 14 chains. Longest chain 13 peptides. Score 0.431 Round 2: 107 peptides, 12 chains. Longest chain 13 peptides. Score 0.497 Round 3: 105 peptides, 11 chains. Longest chain 21 peptides. Score 0.509 Round 4: 93 peptides, 10 chains. Longest chain 20 peptides. Score 0.478 Round 5: 102 peptides, 11 chains. Longest chain 23 peptides. Score 0.496 Taking the results from Round 3 Chains 11, Residues 94, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3187 reflections ( 99.91 % complete ) and 2284 restraints for refining 1090 atoms. 1919 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3048 (Rfree = 0.000) for 1090 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 22: After refmac, R = 0.2949 (Rfree = 0.000) for 1071 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. Cycle 23: After refmac, R = 0.2785 (Rfree = 0.000) for 1065 atoms. Found 5 (5 requested) and removed 6 (2 requested) atoms. Cycle 24: After refmac, R = 0.3058 (Rfree = 0.000) for 1058 atoms. Found 5 (5 requested) and removed 2 (2 requested) atoms. Cycle 25: After refmac, R = 0.2786 (Rfree = 0.000) for 1054 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.72 2.53 Search for helices and strands: 0 residues in 0 chains, 1120 seeds are put forward Round 1: 97 peptides, 14 chains. Longest chain 20 peptides. Score 0.407 Round 2: 98 peptides, 12 chains. Longest chain 14 peptides. Score 0.456 Round 3: 96 peptides, 11 chains. Longest chain 26 peptides. Score 0.469 Round 4: 90 peptides, 11 chains. Longest chain 17 peptides. Score 0.441 Round 5: 92 peptides, 11 chains. Longest chain 15 peptides. Score 0.451 Taking the results from Round 3 Chains 11, Residues 85, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3187 reflections ( 99.91 % complete ) and 2379 restraints for refining 1091 atoms. 2050 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2934 (Rfree = 0.000) for 1091 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. Cycle 27: After refmac, R = 0.2817 (Rfree = 0.000) for 1072 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 28: After refmac, R = 0.2876 (Rfree = 0.000) for 1054 atoms. Found 5 (5 requested) and removed 2 (2 requested) atoms. Cycle 29: After refmac, R = 0.2981 (Rfree = 0.000) for 1044 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. Cycle 30: After refmac, R = 0.2943 (Rfree = 0.000) for 1038 atoms. Found 4 (4 requested) and removed 6 (2 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.84 2.62 Search for helices and strands: 0 residues in 0 chains, 1106 seeds are put forward Round 1: 94 peptides, 15 chains. Longest chain 11 peptides. Score 0.369 Round 2: 104 peptides, 11 chains. Longest chain 20 peptides. Score 0.505 Round 3: 93 peptides, 11 chains. Longest chain 18 peptides. Score 0.455 Round 4: 100 peptides, 11 chains. Longest chain 19 peptides. Score 0.488 Round 5: 95 peptides, 10 chains. Longest chain 20 peptides. Score 0.487 Taking the results from Round 2 Chains 11, Residues 93, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3187 reflections ( 99.91 % complete ) and 2244 restraints for refining 1065 atoms. 1883 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2955 (Rfree = 0.000) for 1065 atoms. Found 5 (5 requested) and removed 12 (2 requested) atoms. Cycle 32: After refmac, R = 0.2852 (Rfree = 0.000) for 1046 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 33: After refmac, R = 0.2807 (Rfree = 0.000) for 1040 atoms. Found 4 (4 requested) and removed 2 (2 requested) atoms. Cycle 34: After refmac, R = 0.2902 (Rfree = 0.000) for 1037 atoms. Found 4 (4 requested) and removed 4 (2 requested) atoms. Cycle 35: After refmac, R = 0.2846 (Rfree = 0.000) for 1036 atoms. Found 4 (4 requested) and removed 5 (2 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.74 2.55 Search for helices and strands: 0 residues in 0 chains, 1112 seeds are put forward Round 1: 84 peptides, 12 chains. Longest chain 16 peptides. Score 0.388 Round 2: 100 peptides, 14 chains. Longest chain 10 peptides. Score 0.422 Round 3: 99 peptides, 11 chains. Longest chain 19 peptides. Score 0.483 Round 4: 102 peptides, 14 chains. Longest chain 12 peptides. Score 0.431 Round 5: 100 peptides, 11 chains. Longest chain 20 peptides. Score 0.488 Taking the results from Round 5 Chains 11, Residues 89, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 3187 reflections ( 99.91 % complete ) and 2259 restraints for refining 1091 atoms. 1896 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2865 (Rfree = 0.000) for 1091 atoms. Found 5 (5 requested) and removed 10 (2 requested) atoms. Cycle 37: After refmac, R = 0.2854 (Rfree = 0.000) for 1070 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 38: After refmac, R = 0.3024 (Rfree = 0.000) for 1059 atoms. Found 5 (5 requested) and removed 6 (2 requested) atoms. Cycle 39: After refmac, R = 0.2822 (Rfree = 0.000) for 1042 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 40: After refmac, R = 0.2678 (Rfree = 0.000) for 1036 atoms. Found 4 (4 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.85 2.62 Search for helices and strands: 0 residues in 0 chains, 1109 seeds are put forward Round 1: 88 peptides, 13 chains. Longest chain 9 peptides. Score 0.385 Round 2: 105 peptides, 15 chains. Longest chain 12 peptides. Score 0.424 Round 3: 104 peptides, 12 chains. Longest chain 23 peptides. Score 0.484 Round 4: 101 peptides, 12 chains. Longest chain 14 peptides. Score 0.470 Round 5: 95 peptides, 12 chains. Longest chain 20 peptides. Score 0.442 Taking the results from Round 3 Chains 14, Residues 92, Estimated correctness of the model 0.0 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 3187 reflections ( 99.91 % complete ) and 2160 restraints for refining 1091 atoms. 1750 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2736 (Rfree = 0.000) for 1091 atoms. Found 5 (5 requested) and removed 8 (2 requested) atoms. Cycle 42: After refmac, R = 0.2803 (Rfree = 0.000) for 1068 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 43: After refmac, R = 0.2769 (Rfree = 0.000) for 1053 atoms. Found 5 (5 requested) and removed 6 (2 requested) atoms. Cycle 44: After refmac, R = 0.2733 (Rfree = 0.000) for 1047 atoms. Found 4 (4 requested) and removed 4 (2 requested) atoms. Cycle 45: After refmac, R = 0.2748 (Rfree = 0.000) for 1041 atoms. Found 4 (4 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.89 2.65 Search for helices and strands: 0 residues in 0 chains, 1108 seeds are put forward Round 1: 90 peptides, 12 chains. Longest chain 15 peptides. Score 0.418 Round 2: 94 peptides, 10 chains. Longest chain 26 peptides. Score 0.482 Round 3: 91 peptides, 10 chains. Longest chain 16 peptides. Score 0.469 Round 4: 93 peptides, 11 chains. Longest chain 15 peptides. Score 0.455 Round 5: 97 peptides, 11 chains. Longest chain 15 peptides. Score 0.474 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 10, Residues 84, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence Sequence coverage is 7 % Consider running further cycles of model building using 1vk9-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3187 reflections ( 99.91 % complete ) and 2350 restraints for refining 1091 atoms. 2014 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2845 (Rfree = 0.000) for 1091 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 47: After refmac, R = 0.2961 (Rfree = 0.000) for 1081 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 48: After refmac, R = 0.2840 (Rfree = 0.000) for 1072 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 49: After refmac, R = 0.2737 (Rfree = 0.000) for 1064 atoms. TimeTaking 31.12